diff --git a/container/README.md b/container/README.md index 8011aa87..acfdc14f 100644 --- a/container/README.md +++ b/container/README.md @@ -48,139 +48,139 @@ On occasion, you may see errors that a download or upload has failed while build ## List of packages -| Package | Homepage | Conda package | Environment | Version | Channel | License | -|:--------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------|:-----------|:-------------------|:---------------------------------------| -| apex | [Link](https://github.com/corbinq/apex) | [Link](https://anaconda.org/dnachun/apex) | apex | 0.2-alpha | dnachun | Other | -| htslib | [Link](http://www.htslib.org/) | [Link](https://anaconda.org/bioconda/htslib) | apex, factor_analysis, bioinfo, methylation, pcatools, pecotmr, quantqtl, tensorqtl | | bioconda | MIT | -| gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | -| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | bioinfo | 2.3.0 | dnachun | GPL‑3.0‑or‑later | -| plink | [Link](https://www.cog-genomics.org/plink2) | [Link](https://anaconda.org/bioconda/plink) | bioinfo | 1.90b6.21 | bioconda | GPL‑3.0‑or‑later | -| plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | -| qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | -| r-bedtoolsr | [Link](https://github.com/PhanstielLab/bedtoolsr) | [Link](https://anaconda.org/bioconda/r-bedtoolsr) | bioinfo | 2.30.0.2 | bioconda | MIT | -| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | -| r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | -| snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | -| snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | -| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL‑3.0‑or‑later | -| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other | -| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT | -| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL‑2.0‑only | -| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL‑3.0‑or‑later | -| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later | -| r-missforest | [Link](https://github.com/stekhoven/missForest) | [Link](https://anaconda.org/conda-forge/r-missforest) | factor_analysis | 1.5 | conda‑forge | GPL‑2.0‑or‑later | -| r-rcppeigen | [Link](https://cran.r-project.org/web/packages/RcppEigen/index.html) | [Link](https://anaconda.org/conda-forge/r-rcppeigen) | factor_analysis | 0.3.3.9.3 | conda‑forge | GPL‑2.0‑or‑later | -| r-snow | [Link](https://github.com/cran/snow) | [Link](https://anaconda.org/conda-forge/r-snow) | factor_analysis | 0.4_4 | conda‑forge | GPL‑2.0‑only | -| r-softimpute | [Link](https://github.com/cran/softImpute) | [Link](https://anaconda.org/conda-forge/r-softimpute) | factor_analysis | 1.4_1 | conda‑forge | GPL‑2.0‑only | -| dap-g | [Link](https://github.com/xqwen/dap) | [Link](https://anaconda.org/dnachun/dap-g) | fastenloc | 1.0.0 | dnachun | AGPL‑3.0‑or‑later | -| fastenloc | [Link](https://github.com/xqwen/fastenloc) | [Link](https://anaconda.org/dnachun/fastenloc) | fastenloc | 2 | dnachun | GPL‑3.0‑or‑later | -| torus | [Link](https://github.com/xqwen/torus) | [Link](https://anaconda.org/dnachun/torus) | fastenloc | 1 | dnachun | Other | -| r-flashpcar | [Link](https://github.com/gabraham/flashpca) | [Link](https://anaconda.org/dnachun/r-flashpcar) | flashpcar | 2.1 | dnachun | GPL‑3.0‑or‑later | -| r-gridextra | [Link](https://cran.r-project.org/web/packages/gridExtra/index.html) | [Link](https://anaconda.org/conda-forge/r-gridextra) | flashpcar | 2.3 | conda‑forge | GPL‑2.0‑or‑later | -| r-matrixstats | [Link](https://cran.rstudio.com/web/packages/matrixStats/index.html) | [Link](https://anaconda.org/conda-forge/r-matrixstats) | flashpcar | 1.0.0 | conda‑forge | Artistic‑2.0 | -| r-rlang | [Link](https://cran.r-project.org/web/packages/rlang/index.html) | [Link](https://anaconda.org/conda-forge/r-rlang) | flashpcar, factor_analysis | 1.1.1 | conda‑forge | GPL‑3.0‑only | -| hello | [Link](https://www.gnu.org/software/hello/) | [Link](https://anaconda.org/dnachun/hello) | hello | 2.12.1 | dnachun | GPL‑3.0‑or‑later | -| r-leafcutter | [Link](https://github.com/davidaknowles/leafcutter) | [Link](https://anaconda.org/dnachun/r-leafcutter) | leafcutter | 0.2.9 | dnachun | GPL‑3.0‑or‑later | -| regtools | [Link](https://github.com/griffithlab/regtools) | [Link](https://anaconda.org/bioconda/regtools) | leafcutter | 1.0.0 | bioconda | MIT | -| metal | [Link](https://github.com/statgen/METAL) | [Link](https://anaconda.org/dnachun/metal) | metal | 2020_05_05 | dnachun | BSD‑3‑Clause | -| bioconductor-illuminahumanmethylation450kmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylation450kmanifest) | methylation | 0.4.0 | bioconda | Artistic‑2.0 | -| bioconductor-illuminahumanmethylationepicmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylationepicmanifest) | methylation | 0.3.0 | bioconda | Artistic‑2.0 | -| bioconductor-limma | [Link](https://bioconductor.org/packages/release/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | methylation | 3.56.2 | bioconda | GPL‑2.0‑or‑later | -| bioconductor-minfi | [Link](https://bioconductor.org/packages/release/bioc/html/minfi.html) | [Link](https://anaconda.org/bioconda/bioconductor-minfi) | methylation | 1.46.0 | bioconda | Artistic‑2.0 | -| bioconductor-preprocesscore | [Link](https://bioconductor.org/packages/release/bioc/html/preprocessCore.html) | [Link](https://anaconda.org/bioconda/bioconductor-preprocesscore) | methylation | 1.62.1 | bioconda | LGPL‑2.0‑or‑later | -| bioconductor-sesame | [Link](https://www.bioconductor.org/packages/release/bioc/html/sesame.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesame) | methylation | 1.18.4 | bioconda | MIT AND Other | -| bioconductor-sesamedata | [Link](https://bioconductor.org/packages/release/data/experiment/html/sesameData.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesamedata) | methylation | 1.18.0 | bioconda | Artistic‑2.0 | -| r-glmnet | [Link](https://cran.r-project.org/web/packages/glmnet/index.html) | [Link](https://anaconda.org/r/r-glmnet) | methylation | 4.1 | conda‑forge | GPL‑2.0‑or‑later | -| r-data.table | [Link](https://cran.r-project.org/web/packages/data.table/index.html) | [Link](https://anaconda.org/conda-forge/r-data.table) | methylation, quantqtl | 1.14.8 | conda‑forge | MPL‑2.0 | -| bioconductor-biocsingular | [Link](https://bioconductor.org/packages/release/bioc/html/BiocSingular.html) | [Link](https://anaconda.org/bioconda/bioconductor-biocsingular) | pcatools | 1.16.0 | bioconda | GPL‑3.0‑or‑later | -| bioconductor-pcatools | [Link](https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html) | [Link](https://anaconda.org/bioconda/bioconductor-pcatools) | pcatools | 2.12.0 | bioconda | GPL‑3.0‑or‑later | -| r-rmtstat | [Link](https://cran.r-project.org/web/packages/RMTstat/index.html) | [Link](https://anaconda.org/conda-forge/r-rmtstat) | pcatools | 0.3.1 | conda‑forge | BSD‑3‑Clause | -| r-fsusier | [Link](https://github.com/stephenslab/fsusier) | [Link](https://anaconda.org/dnachun/r-fsusier) | pecotmr | 0.2.0 | dnachun | GPL‑3.0‑or‑later | -| r-mvsusier | [Link](https://github.com/stephenslab/mvsusieR) | [Link](https://anaconda.org/dnachun/r-mvsusier) | pecotmr | 0.1.7 | dnachun | GPL‑3.0‑or‑later | -| r-pecotmr | [Link](https://github.com/cumc/pecotmr) | [Link](https://anaconda.org/dnachun/r-pecotmr) | pecotmr | 0.1.56 | dnachun | GPL‑3.0‑or‑later | -| r-susier | [Link](https://github.com/stephenslab/susieR) | [Link](https://anaconda.org/conda-forge/r-susier) | pecotmr, fastenloc | 0.14.7 | conda‑forge | MIT | -| backports.zoneinfo | [Link](https://pypi.org/project/backports.zoneinfo/) | [Link](https://anaconda.org/conda-forge/backports.zoneinfo) | pecotmr, quantqtl | 0.2.1 | conda‑forge | Apache‑2.0 | -| bioconductor-variantannotation | [Link](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) | [Link](https://anaconda.org/bioconda/bioconductor-variantannotation) | pecotmr, quantqtl | 1.48.1 | bioconda | Artistic‑2.0 | -| python-ldstore | [Link](https://pypi.org/project/ldstore/) | [Link](https://anaconda.org/dnachun/python-ldstore) | pecotmr, quantqtl | 0.1.9 | dnachun | MIT | -| r-complexupset | [Link](https://cran.r-project.org/web/packages/ComplexUpset/index.html) | [Link](https://anaconda.org/conda-forge/r-complexupset) | pecotmr, quantqtl | 1.3.3 | conda‑forge | MIT | -| r-cowplot | [Link](https://cran.r-project.org/web/packages/cowplot/index.html) | [Link](https://anaconda.org/conda-forge/r-cowplot) | pecotmr, quantqtl | 1.1.1 | conda‑forge | GPL‑2.0‑only | -| r-genio | [Link](https://cran.r-project.org/web/packages/genio/index.html) | [Link](https://anaconda.org/dnachun/r-genio) | pecotmr, quantqtl | 1.1.2 | dnachun | GPL‑3.0‑or‑later | -| r-gwasrapidd | [Link](https://cran.r-project.com/web/packages/gwasrapidd/index.html) | [Link](https://anaconda.org/dnachun/r-gwasrapidd) | pecotmr, quantqtl | 0.99.14 | dnachun | MIT | -| r-udr | [Link](https://github.com/stephenslab/udr) | [Link](https://anaconda.org/dnachun/r-udr) | pecotmr, quantqtl | 0.3.154 | dnachun | BSD‑3‑Clause | -| finemap | [Link](http://christianbenner.com) | [Link](https://anaconda.org/bioconda/finemap) | polyfun | 1.4.1 | bioconda | Other | -| ldstore | [Link](http://christianbenner.com) | [Link](https://anaconda.org/dnachun/ldstore) | polyfun | 2 | dnachun | Other | -| polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT | -| bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | -| suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | -| r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause | -| r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other | -| r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later | -| r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | GPL‑2.0‑or‑later | -| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | -| r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | -| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | -| ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | dnachun | Apache‑2.0 | -| r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | -| bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | -| bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | -| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | bioconda | GPL‑3.0‑or‑later | -| fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | -| fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | -| gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | -| gtex-pipeline-gene_model | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-gene_model) | rna_quantification | gtex_v8 | dnachun | Other | -| gtex-pipeline-qtl | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-qtl) | rna_quantification | gtex_v8 | dnachun | Other | -| gtex-pipeline-rnaseq | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) | [Link](https://anaconda.org/dnachun/gtex-pipeline-rnaseq) | rna_quantification | gtex_v8 | dnachun | Other | -| kallisto | [Link](https://github.com/pachterlab/kallisto) | [Link](https://anaconda.org/bioconda/kallisto) | rna_quantification | 0.50.0 | bioconda | BSD‑2‑Clause | -| kent-tools | [Link](https://genome.ucsc.edu/) | [Link](https://anaconda.org/dnachun/kent-tools) | rna_quantification | 438 | dnachun | MIT | -| multiqc | [Link](https://github.com/ewels/MultiQC) | [Link](https://anaconda.org/bioconda/multiqc) | rna_quantification | 1.15 | bioconda | GPL‑3.0‑or‑later | -| picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | -| pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | -| pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | -| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | -| rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | -| rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | -| star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11b | bioconda | GPL‑3.0‑or‑later | -| trimmomatic | [Link](https://github.com/timflutre/trimmomatic) | [Link](https://anaconda.org/bioconda/trimmomatic) | rna_quantification | 0.39 | bioconda | GPL‑3.0‑or‑later | -| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | rna_quantification, tensorqtl, quantqtl | 1.3.5 | conda‑forge | BSD‑3‑Clause | -| bioconductor-edger | [Link](https://bioconductor.org/packages/3.18/bioc/html/edgeR.html) | [Link](https://anaconda.org/bioconda/bioconductor-edger) | seurat | 4.0.2 | bioconda | GPL‑2.0‑or‑later | -| bioconductor-limma | [Link](https://bioconductor.org/packages/3.18/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | seurat | 3.58.1 | bioconda | GPL‑2.0‑or‑later | -| r-seurat | [Link](https://satijalab.org/seurat) | [Link](https://anaconda.org/conda-forge/r-seurat) | seurat | 5.0.1 | conda‑forge | MIT | -| bioconductor-qvalue | [Link](https://www.bioconductor.org/packages/release/bioc/html/qvalue.html) | [Link](https://anaconda.org/bioconda/bioconductor-qvalue) | tensorqtl | 2.32.0 | bioconda | LGPL‑3.0‑or‑later | -| multipy | [Link](https://github.com/puolival/multipy) | [Link](https://anaconda.org/dnachun/multipy) | tensorqtl | 0.16 | dnachun | BSD‑3‑Clause | -| qvalue | [Link](https://pypi.org/project/qvalue/) | [Link](https://anaconda.org/dnachun/qvalue) | tensorqtl | 0.1.3 | bioconda | BSD‑3‑Clause | -| tensorqtl | [Link](https://github.com/broadinstitute/tensorqtl) | [Link](https://anaconda.org/dnachun/tensorqtl) | tensorqtl | 1.0.8 | dnachun | BSD‑3‑Clause | -| altair | [Link](https://pypi.org/project/altair/) | [Link](https://anaconda.org/conda-forge/altair) | universal | | conda‑forge | BSD‑3‑Clause | -| awscli | [Link](https://github.com/aws/aws-cli) | [Link](https://anaconda.org/conda-forge/awscli) | universal | | conda‑forge | Apache‑2.0 | -| bash_kernel | [Link](https://github.com/takluyver/bash_kernel) | [Link](https://anaconda.org/conda-forge/bash_kernel) | universal | | conda‑forge | BSD‑3‑Clause | -| feather-format | [Link](https://pypi.org/project/feather-format/) | [Link](https://anaconda.org/conda-forge/feather-format) | universal | | conda‑forge | Apache‑2.0 | -| formulaic | [Link](https://github.com/matthewwardrop/formulaic) | [Link](https://anaconda.org/conda-forge/formulaic) | universal | | conda‑forge | MIT | -| imageio | [Link](https://pypi.org/project/imageio/) | [Link](https://anaconda.org/conda-forge/imageio) | universal | | conda‑forge | BSD‑2‑Clause | -| ipykernel | [Link](https://pypi.org/project/ipykernel/) | [Link](https://anaconda.org/conda-forge/ipykernel) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyter_contrib_nbextensions | [Link](https://pypi.org/project/jupyter-contrib-nbextensions/) | [Link](https://anaconda.org/conda-forge/jupyter_contrib_nbextensions) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyterlab | [Link](https://pypi.org/project/jupyterlab/) | [Link](https://anaconda.org/conda-forge/jupyterlab) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyterlab-sos | [Link](https://pypi.org/project/jupyterlab-sos/) | [Link](https://anaconda.org/conda-forge/jupyterlab-sos) | universal | | conda‑forge | BSD‑3‑Clause | -| markdown-kernel | [Link](https://pypi.org/project/markdown-kernel/) | [Link](https://anaconda.org/conda-forge/markdown-kernel) | universal | | conda‑forge | BSD‑3‑Clause | -| matplotlib | [Link](https://pypi.org/project/matplotlib/) | [Link](https://anaconda.org/conda-forge/matplotlib) | universal | | conda‑forge | PSF‑2.0 AND CC0‑1.0 | -| nbdime | [Link](https://pypi.org/project/nbdime/) | [Link](https://anaconda.org/conda-forge/nbdime) | universal | | conda‑forge | BSD‑3‑Clause | -| notebook | [Link](https://pypi.org/project/notebook/) | [Link](https://anaconda.org/conda-forge/notebook) | universal | | conda‑forge | BSD‑3‑Clause | -| numpy | [Link](https://pypi.org/project/numpy/) | [Link](https://anaconda.org/conda-forge/numpy) | universal | | conda‑forge | BSD‑3‑Clause | -| openpyxl | [Link](https://pypi.org/project/openpyxl/) | [Link](https://anaconda.org/conda-forge/openpyxl) | universal | | conda‑forge | MIT | -| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | universal | | conda‑forge | BSD‑3‑Clause | -| parallel | [Link](https://www.gnu.org/software/parallel/) | [Link](https://anaconda.org/conda-forge/parallel) | universal | | conda‑forge | GPL‑3.0‑or‑later | -| plotnine | [Link](https://pypi.org/project/plotnine/) | [Link](https://anaconda.org/conda-forge/plotnine) | universal | | conda‑forge | MIT | -| ptpython | [Link](https://pypi.org/project/ptpython/) | [Link](https://anaconda.org/conda-forge/ptpython) | universal | | conda‑forge | BSD‑3‑Clause | -| pytables | [Link](https://pypi.org/project/tables/) | [Link](https://anaconda.org/conda-forge/pytables) | universal | | conda‑forge | BSD‑3‑Clause | -| r-irkernel | [Link](https://cran.rstudio.com/web/packages/IRkernel/index.html) | [Link](https://anaconda.org/conda-forge/r-irkernel) | universal | | conda‑forge | MIT | -| r-languageserver | [Link](https://cran.r-project.org/web/packages/languageserver/index.html) | [Link](https://anaconda.org/search?q=r-languageserver) | universal | | conda‑forge | MIT | -| r-tidyverse | [Link](https://cran.r-project.org/web/packages/tidyverse/index.html) | [Link](https://anaconda.org/conda-forge/r-tidyverse) | universal | | conda‑forge | MIT | -| rpy2 | [Link](https://pypi.org/project/rpy2/) | [Link](https://anaconda.org/conda-forge/rpy2) | universal | | conda‑forge | GPL‑2.0‑or‑later | -| scikit-learn | [Link](https://pypi.org/project/scikit-learn/) | [Link](https://anaconda.org/conda-forge/scikit-learn) | universal | | conda‑forge | BSD‑3‑Clause | -| scipy | [Link](https://pypi.org/project/scipy/) | [Link](https://anaconda.org/conda-forge/scipy) | universal | | conda‑forge | BSD‑3‑Clause | -| seaborn | [Link](https://pypi.org/project/seaborn/) | [Link](https://anaconda.org/conda-forge/seaborn) | universal | | conda‑forge | BSD‑3‑Clause | -| sos | [Link](https://pypi.org/project/sos/) | [Link](https://anaconda.org/conda-forge/sos) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-bash | [Link](https://pypi.org/project/sos-bash/) | [Link](https://anaconda.org/conda-forge/sos-bash) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-notebook | [Link](https://pypi.org/project/sos-notebook/) | [Link](https://anaconda.org/conda-forge/sos-notebook) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-pbs | [Link](https://pypi.org/project/sos-pbs/) | [Link](https://anaconda.org/conda-forge/sos-pbs) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-python | [Link](https://pypi.org/project/sos-python/) | [Link](https://anaconda.org/conda-forge/sos-python) | universal | | conda‑forge | BSD‑3‑Clause | -| statsmodels | [Link](https://pypi.org/project/statsmodels/) | [Link](https://anaconda.org/conda-forge/statsmodels) | universal | | conda‑forge | BSD‑3‑Clause | -| wand | [Link](https://pypi.org/project/wand/) | [Link](https://anaconda.org/conda-forge/wand) | universal | | conda‑forge | BSD‑3‑Clause | \ No newline at end of file +| Package | Homepage | Conda package | Environment | Version | Channel | License | +|:--------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------|:-----------|:-------------------|:---------------------------------------| +| apex | [Link](https://github.com/corbinq/apex) | [Link](https://anaconda.org/dnachun/apex) | apex | 0.2-alpha | dnachun | Other | +| htslib | [Link](http://www.htslib.org/) | [Link](https://anaconda.org/bioconda/htslib) | apex, factor_analysis, bioinfo, methylation, pcatools, pecotmr, quantqtl, tensorqtl, rna_quantification | | bioconda | MIT | +| gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | +| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | bioinfo | 2.3.0 | dnachun | GPL‑3.0‑or‑later | +| plink | [Link](https://www.cog-genomics.org/plink2) | [Link](https://anaconda.org/bioconda/plink) | bioinfo | 1.90b6.21 | bioconda | GPL‑3.0‑or‑later | +| plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | +| qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | +| r-bedtoolsr | [Link](https://github.com/PhanstielLab/bedtoolsr) | [Link](https://anaconda.org/bioconda/r-bedtoolsr) | bioinfo | 2.30.0.2 | bioconda | MIT | +| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | +| r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | +| snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | +| snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | +| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL‑3.0‑or‑later | +| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other | +| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT | +| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL‑2.0‑only | +| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL‑3.0‑or‑later | +| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later | +| r-missforest | [Link](https://github.com/stekhoven/missForest) | [Link](https://anaconda.org/conda-forge/r-missforest) | factor_analysis | 1.5 | conda‑forge | GPL‑2.0‑or‑later | +| r-rcppeigen | [Link](https://cran.r-project.org/web/packages/RcppEigen/index.html) | [Link](https://anaconda.org/conda-forge/r-rcppeigen) | factor_analysis | 0.3.3.9.3 | conda‑forge | GPL‑2.0‑or‑later | +| r-snow | [Link](https://github.com/cran/snow) | [Link](https://anaconda.org/conda-forge/r-snow) | factor_analysis | 0.4_4 | conda‑forge | GPL‑2.0‑only | +| r-softimpute | [Link](https://github.com/cran/softImpute) | [Link](https://anaconda.org/conda-forge/r-softimpute) | factor_analysis | 1.4_1 | conda‑forge | GPL‑2.0‑only | +| dap-g | [Link](https://github.com/xqwen/dap) | [Link](https://anaconda.org/dnachun/dap-g) | fastenloc | 1.0.0 | dnachun | AGPL‑3.0‑or‑later | +| fastenloc | [Link](https://github.com/xqwen/fastenloc) | [Link](https://anaconda.org/dnachun/fastenloc) | fastenloc | 2 | dnachun | GPL‑3.0‑or‑later | +| torus | [Link](https://github.com/xqwen/torus) | [Link](https://anaconda.org/dnachun/torus) | fastenloc | 1 | dnachun | Other | +| r-flashpcar | [Link](https://github.com/gabraham/flashpca) | [Link](https://anaconda.org/dnachun/r-flashpcar) | flashpcar | 2.1 | dnachun | GPL‑3.0‑or‑later | +| r-gridextra | [Link](https://cran.r-project.org/web/packages/gridExtra/index.html) | [Link](https://anaconda.org/conda-forge/r-gridextra) | flashpcar | 2.3 | conda‑forge | GPL‑2.0‑or‑later | +| r-matrixstats | [Link](https://cran.rstudio.com/web/packages/matrixStats/index.html) | [Link](https://anaconda.org/conda-forge/r-matrixstats) | flashpcar | 1.0.0 | conda‑forge | Artistic‑2.0 | +| r-rlang | [Link](https://cran.r-project.org/web/packages/rlang/index.html) | [Link](https://anaconda.org/conda-forge/r-rlang) | flashpcar, factor_analysis | 1.1.1 | conda‑forge | GPL‑3.0‑only | +| hello | [Link](https://www.gnu.org/software/hello/) | [Link](https://anaconda.org/dnachun/hello) | hello | 2.12.1 | dnachun | GPL‑3.0‑or‑later | +| r-leafcutter | [Link](https://github.com/davidaknowles/leafcutter) | [Link](https://anaconda.org/dnachun/r-leafcutter) | leafcutter | 0.2.9 | dnachun | GPL‑3.0‑or‑later | +| regtools | [Link](https://github.com/griffithlab/regtools) | [Link](https://anaconda.org/bioconda/regtools) | leafcutter | 1.0.0 | bioconda | MIT | +| metal | [Link](https://github.com/statgen/METAL) | [Link](https://anaconda.org/dnachun/metal) | metal | 2020_05_05 | dnachun | BSD‑3‑Clause | +| bioconductor-illuminahumanmethylation450kmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylation450kmanifest) | methylation | 0.4.0 | bioconda | Artistic‑2.0 | +| bioconductor-illuminahumanmethylationepicmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylationepicmanifest) | methylation | 0.3.0 | bioconda | Artistic‑2.0 | +| bioconductor-limma | [Link](https://bioconductor.org/packages/release/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | methylation | 3.56.2 | bioconda | GPL‑2.0‑or‑later | +| bioconductor-minfi | [Link](https://bioconductor.org/packages/release/bioc/html/minfi.html) | [Link](https://anaconda.org/bioconda/bioconductor-minfi) | methylation | 1.46.0 | bioconda | Artistic‑2.0 | +| bioconductor-preprocesscore | [Link](https://bioconductor.org/packages/release/bioc/html/preprocessCore.html) | [Link](https://anaconda.org/bioconda/bioconductor-preprocesscore) | methylation | 1.62.1 | bioconda | LGPL‑2.0‑or‑later | +| bioconductor-sesame | [Link](https://www.bioconductor.org/packages/release/bioc/html/sesame.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesame) | methylation | 1.18.4 | bioconda | MIT AND Other | +| bioconductor-sesamedata | [Link](https://bioconductor.org/packages/release/data/experiment/html/sesameData.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesamedata) | methylation | 1.18.0 | bioconda | Artistic‑2.0 | +| r-glmnet | [Link](https://cran.r-project.org/web/packages/glmnet/index.html) | [Link](https://anaconda.org/r/r-glmnet) | methylation | 4.1 | conda‑forge | GPL‑2.0‑or‑later | +| r-data.table | [Link](https://cran.r-project.org/web/packages/data.table/index.html) | [Link](https://anaconda.org/conda-forge/r-data.table) | methylation, quantqtl | 1.14.8 | conda‑forge | MPL‑2.0 | +| bioconductor-biocsingular | [Link](https://bioconductor.org/packages/release/bioc/html/BiocSingular.html) | [Link](https://anaconda.org/bioconda/bioconductor-biocsingular) | pcatools | 1.16.0 | bioconda | GPL‑3.0‑or‑later | +| bioconductor-pcatools | [Link](https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html) | [Link](https://anaconda.org/bioconda/bioconductor-pcatools) | pcatools | 2.12.0 | bioconda | GPL‑3.0‑or‑later | +| r-rmtstat | [Link](https://cran.r-project.org/web/packages/RMTstat/index.html) | [Link](https://anaconda.org/conda-forge/r-rmtstat) | pcatools | 0.3.1 | conda‑forge | BSD‑3‑Clause | +| r-fsusier | [Link](https://github.com/stephenslab/fsusier) | [Link](https://anaconda.org/dnachun/r-fsusier) | pecotmr | 0.2.0 | dnachun | GPL‑3.0‑or‑later | +| r-mvsusier | [Link](https://github.com/stephenslab/mvsusieR) | [Link](https://anaconda.org/dnachun/r-mvsusier) | pecotmr | 0.1.7 | dnachun | GPL‑3.0‑or‑later | +| r-pecotmr | [Link](https://github.com/cumc/pecotmr) | [Link](https://anaconda.org/dnachun/r-pecotmr) | pecotmr | 0.1.56 | dnachun | GPL‑3.0‑or‑later | +| r-susier | [Link](https://github.com/stephenslab/susieR) | [Link](https://anaconda.org/conda-forge/r-susier) | pecotmr, fastenloc | 0.14.7 | conda‑forge | MIT | +| backports.zoneinfo | [Link](https://pypi.org/project/backports.zoneinfo/) | [Link](https://anaconda.org/conda-forge/backports.zoneinfo) | pecotmr, quantqtl | 0.2.1 | conda‑forge | Apache‑2.0 | +| bioconductor-variantannotation | [Link](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) | [Link](https://anaconda.org/bioconda/bioconductor-variantannotation) | pecotmr, quantqtl | 1.48.1 | bioconda | Artistic‑2.0 | +| python-ldstore | [Link](https://pypi.org/project/ldstore/) | [Link](https://anaconda.org/dnachun/python-ldstore) | pecotmr, quantqtl | 0.1.9 | dnachun | MIT | +| r-complexupset | [Link](https://cran.r-project.org/web/packages/ComplexUpset/index.html) | [Link](https://anaconda.org/conda-forge/r-complexupset) | pecotmr, quantqtl | 1.3.3 | conda‑forge | MIT | +| r-cowplot | [Link](https://cran.r-project.org/web/packages/cowplot/index.html) | [Link](https://anaconda.org/conda-forge/r-cowplot) | pecotmr, quantqtl | 1.1.1 | conda‑forge | GPL‑2.0‑only | +| r-genio | [Link](https://cran.r-project.org/web/packages/genio/index.html) | [Link](https://anaconda.org/dnachun/r-genio) | pecotmr, quantqtl | 1.1.2 | dnachun | GPL‑3.0‑or‑later | +| r-gwasrapidd | [Link](https://cran.r-project.com/web/packages/gwasrapidd/index.html) | [Link](https://anaconda.org/dnachun/r-gwasrapidd) | pecotmr, quantqtl | 0.99.14 | dnachun | MIT | +| r-udr | [Link](https://github.com/stephenslab/udr) | [Link](https://anaconda.org/dnachun/r-udr) | pecotmr, quantqtl | 0.3.154 | dnachun | BSD‑3‑Clause | +| finemap | [Link](http://christianbenner.com) | [Link](https://anaconda.org/bioconda/finemap) | polyfun | 1.4.1 | bioconda | Other | +| ldstore | [Link](http://christianbenner.com) | [Link](https://anaconda.org/dnachun/ldstore) | polyfun | 2 | dnachun | Other | +| polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT | +| bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | +| suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | +| r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause | +| r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other | +| r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later | +| r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | GPL‑2.0‑or‑later | +| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | +| r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | +| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | +| ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | dnachun | Apache‑2.0 | +| r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | +| bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | +| bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | bioconda | GPL‑3.0‑or‑later | +| fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | +| fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | +| gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | +| gtex-pipeline-gene_model | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-gene_model) | rna_quantification | gtex_v8 | dnachun | Other | +| gtex-pipeline-qtl | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-qtl) | rna_quantification | gtex_v8 | dnachun | Other | +| gtex-pipeline-rnaseq | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) | [Link](https://anaconda.org/dnachun/gtex-pipeline-rnaseq) | rna_quantification | gtex_v8 | dnachun | Other | +| kallisto | [Link](https://github.com/pachterlab/kallisto) | [Link](https://anaconda.org/bioconda/kallisto) | rna_quantification | 0.50.0 | bioconda | BSD‑2‑Clause | +| kent-tools | [Link](https://genome.ucsc.edu/) | [Link](https://anaconda.org/dnachun/kent-tools) | rna_quantification | 438 | dnachun | MIT | +| multiqc | [Link](https://github.com/ewels/MultiQC) | [Link](https://anaconda.org/bioconda/multiqc) | rna_quantification | 1.15 | bioconda | GPL‑3.0‑or‑later | +| picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | +| pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | +| pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | +| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | +| rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | +| rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | +| star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11b | bioconda | GPL‑3.0‑or‑later | +| trimmomatic | [Link](https://github.com/timflutre/trimmomatic) | [Link](https://anaconda.org/bioconda/trimmomatic) | rna_quantification | 0.39 | bioconda | GPL‑3.0‑or‑later | +| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | rna_quantification, tensorqtl, quantqtl | 1.3.5 | conda‑forge | BSD‑3‑Clause | +| bioconductor-edger | [Link](https://bioconductor.org/packages/3.18/bioc/html/edgeR.html) | [Link](https://anaconda.org/bioconda/bioconductor-edger) | seurat | 4.0.2 | bioconda | GPL‑2.0‑or‑later | +| bioconductor-limma | [Link](https://bioconductor.org/packages/3.18/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | seurat | 3.58.1 | bioconda | GPL‑2.0‑or‑later | +| r-seurat | [Link](https://satijalab.org/seurat) | [Link](https://anaconda.org/conda-forge/r-seurat) | seurat | 5.0.1 | conda‑forge | MIT | +| bioconductor-qvalue | [Link](https://www.bioconductor.org/packages/release/bioc/html/qvalue.html) | [Link](https://anaconda.org/bioconda/bioconductor-qvalue) | tensorqtl | 2.32.0 | bioconda | LGPL‑3.0‑or‑later | +| multipy | [Link](https://github.com/puolival/multipy) | [Link](https://anaconda.org/dnachun/multipy) | tensorqtl | 0.16 | dnachun | BSD‑3‑Clause | +| qvalue | [Link](https://pypi.org/project/qvalue/) | [Link](https://anaconda.org/dnachun/qvalue) | tensorqtl | 0.1.3 | bioconda | BSD‑3‑Clause | +| tensorqtl | [Link](https://github.com/broadinstitute/tensorqtl) | [Link](https://anaconda.org/dnachun/tensorqtl) | tensorqtl | 1.0.8 | dnachun | BSD‑3‑Clause | +| altair | [Link](https://pypi.org/project/altair/) | [Link](https://anaconda.org/conda-forge/altair) | universal | | conda‑forge | BSD‑3‑Clause | +| awscli | [Link](https://github.com/aws/aws-cli) | [Link](https://anaconda.org/conda-forge/awscli) | universal | | conda‑forge | Apache‑2.0 | +| bash_kernel | [Link](https://github.com/takluyver/bash_kernel) | [Link](https://anaconda.org/conda-forge/bash_kernel) | universal | | conda‑forge | BSD‑3‑Clause | +| feather-format | [Link](https://pypi.org/project/feather-format/) | [Link](https://anaconda.org/conda-forge/feather-format) | universal | | conda‑forge | Apache‑2.0 | +| formulaic | [Link](https://github.com/matthewwardrop/formulaic) | [Link](https://anaconda.org/conda-forge/formulaic) | universal | | conda‑forge | MIT | +| imageio | [Link](https://pypi.org/project/imageio/) | [Link](https://anaconda.org/conda-forge/imageio) | universal | | conda‑forge | BSD‑2‑Clause | +| ipykernel | [Link](https://pypi.org/project/ipykernel/) | [Link](https://anaconda.org/conda-forge/ipykernel) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyter_contrib_nbextensions | [Link](https://pypi.org/project/jupyter-contrib-nbextensions/) | [Link](https://anaconda.org/conda-forge/jupyter_contrib_nbextensions) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyterlab | [Link](https://pypi.org/project/jupyterlab/) | [Link](https://anaconda.org/conda-forge/jupyterlab) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyterlab-sos | [Link](https://pypi.org/project/jupyterlab-sos/) | [Link](https://anaconda.org/conda-forge/jupyterlab-sos) | universal | | conda‑forge | BSD‑3‑Clause | +| markdown-kernel | [Link](https://pypi.org/project/markdown-kernel/) | [Link](https://anaconda.org/conda-forge/markdown-kernel) | universal | | conda‑forge | BSD‑3‑Clause | +| matplotlib | [Link](https://pypi.org/project/matplotlib/) | [Link](https://anaconda.org/conda-forge/matplotlib) | universal | | conda‑forge | PSF‑2.0 AND CC0‑1.0 | +| nbdime | [Link](https://pypi.org/project/nbdime/) | [Link](https://anaconda.org/conda-forge/nbdime) | universal | | conda‑forge | BSD‑3‑Clause | +| notebook | [Link](https://pypi.org/project/notebook/) | [Link](https://anaconda.org/conda-forge/notebook) | universal | | conda‑forge | BSD‑3‑Clause | +| numpy | [Link](https://pypi.org/project/numpy/) | [Link](https://anaconda.org/conda-forge/numpy) | universal | | conda‑forge | BSD‑3‑Clause | +| openpyxl | [Link](https://pypi.org/project/openpyxl/) | [Link](https://anaconda.org/conda-forge/openpyxl) | universal | | conda‑forge | MIT | +| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | universal | | conda‑forge | BSD‑3‑Clause | +| parallel | [Link](https://www.gnu.org/software/parallel/) | [Link](https://anaconda.org/conda-forge/parallel) | universal | | conda‑forge | GPL‑3.0‑or‑later | +| plotnine | [Link](https://pypi.org/project/plotnine/) | [Link](https://anaconda.org/conda-forge/plotnine) | universal | | conda‑forge | MIT | +| ptpython | [Link](https://pypi.org/project/ptpython/) | [Link](https://anaconda.org/conda-forge/ptpython) | universal | | conda‑forge | BSD‑3‑Clause | +| pytables | [Link](https://pypi.org/project/tables/) | [Link](https://anaconda.org/conda-forge/pytables) | universal | | conda‑forge | BSD‑3‑Clause | +| r-irkernel | [Link](https://cran.rstudio.com/web/packages/IRkernel/index.html) | [Link](https://anaconda.org/conda-forge/r-irkernel) | universal | | conda‑forge | MIT | +| r-languageserver | [Link](https://cran.r-project.org/web/packages/languageserver/index.html) | [Link](https://anaconda.org/search?q=r-languageserver) | universal | | conda‑forge | MIT | +| r-tidyverse | [Link](https://cran.r-project.org/web/packages/tidyverse/index.html) | [Link](https://anaconda.org/conda-forge/r-tidyverse) | universal | | conda‑forge | MIT | +| rpy2 | [Link](https://pypi.org/project/rpy2/) | [Link](https://anaconda.org/conda-forge/rpy2) | universal | | conda‑forge | GPL‑2.0‑or‑later | +| scikit-learn | [Link](https://pypi.org/project/scikit-learn/) | [Link](https://anaconda.org/conda-forge/scikit-learn) | universal | | conda‑forge | BSD‑3‑Clause | +| scipy | [Link](https://pypi.org/project/scipy/) | [Link](https://anaconda.org/conda-forge/scipy) | universal | | conda‑forge | BSD‑3‑Clause | +| seaborn | [Link](https://pypi.org/project/seaborn/) | [Link](https://anaconda.org/conda-forge/seaborn) | universal | | conda‑forge | BSD‑3‑Clause | +| sos | [Link](https://pypi.org/project/sos/) | [Link](https://anaconda.org/conda-forge/sos) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-bash | [Link](https://pypi.org/project/sos-bash/) | [Link](https://anaconda.org/conda-forge/sos-bash) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-notebook | [Link](https://pypi.org/project/sos-notebook/) | [Link](https://anaconda.org/conda-forge/sos-notebook) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-pbs | [Link](https://pypi.org/project/sos-pbs/) | [Link](https://anaconda.org/conda-forge/sos-pbs) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-python | [Link](https://pypi.org/project/sos-python/) | [Link](https://anaconda.org/conda-forge/sos-python) | universal | | conda‑forge | BSD‑3‑Clause | +| statsmodels | [Link](https://pypi.org/project/statsmodels/) | [Link](https://anaconda.org/conda-forge/statsmodels) | universal | | conda‑forge | BSD‑3‑Clause | +| wand | [Link](https://pypi.org/project/wand/) | [Link](https://anaconda.org/conda-forge/wand) | universal | | conda‑forge | BSD‑3‑Clause | \ No newline at end of file diff --git a/container/readme/containers.md b/container/readme/containers.md index 2a5c1c6a..a6171b53 100644 --- a/container/readme/containers.md +++ b/container/readme/containers.md @@ -1,136 +1,136 @@ -| Package | Homepage | Conda package | Environment | Version | Channel | License | -|:--------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------|:-----------|:-------------------|:---------------------------------------| -| apex | [Link](https://github.com/corbinq/apex) | [Link](https://anaconda.org/dnachun/apex) | apex | 0.2-alpha | dnachun | Other | -| htslib | [Link](http://www.htslib.org/) | [Link](https://anaconda.org/bioconda/htslib) | apex, factor_analysis, bioinfo, methylation, pcatools, pecotmr, quantqtl, tensorqtl | | bioconda | MIT | -| gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | -| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | bioinfo | 2.3.0 | dnachun | GPL‑3.0‑or‑later | -| plink | [Link](https://www.cog-genomics.org/plink2) | [Link](https://anaconda.org/bioconda/plink) | bioinfo | 1.90b6.21 | bioconda | GPL‑3.0‑or‑later | -| plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | -| qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | -| r-bedtoolsr | [Link](https://github.com/PhanstielLab/bedtoolsr) | [Link](https://anaconda.org/bioconda/r-bedtoolsr) | bioinfo | 2.30.0.2 | bioconda | MIT | -| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | -| r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | -| snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | -| snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | -| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL‑3.0‑or‑later | -| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other | -| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT | -| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL‑2.0‑only | -| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL‑3.0‑or‑later | -| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later | -| r-missforest | [Link](https://github.com/stekhoven/missForest) | [Link](https://anaconda.org/conda-forge/r-missforest) | factor_analysis | 1.5 | conda‑forge | GPL‑2.0‑or‑later | -| r-rcppeigen | [Link](https://cran.r-project.org/web/packages/RcppEigen/index.html) | [Link](https://anaconda.org/conda-forge/r-rcppeigen) | factor_analysis | 0.3.3.9.3 | conda‑forge | GPL‑2.0‑or‑later | -| r-snow | [Link](https://github.com/cran/snow) | [Link](https://anaconda.org/conda-forge/r-snow) | factor_analysis | 0.4_4 | conda‑forge | GPL‑2.0‑only | -| r-softimpute | [Link](https://github.com/cran/softImpute) | [Link](https://anaconda.org/conda-forge/r-softimpute) | factor_analysis | 1.4_1 | conda‑forge | GPL‑2.0‑only | -| dap-g | [Link](https://github.com/xqwen/dap) | [Link](https://anaconda.org/dnachun/dap-g) | fastenloc | 1.0.0 | dnachun | AGPL‑3.0‑or‑later | -| fastenloc | [Link](https://github.com/xqwen/fastenloc) | [Link](https://anaconda.org/dnachun/fastenloc) | fastenloc | 2 | dnachun | GPL‑3.0‑or‑later | -| torus | [Link](https://github.com/xqwen/torus) | [Link](https://anaconda.org/dnachun/torus) | fastenloc | 1 | dnachun | Other | -| r-flashpcar | [Link](https://github.com/gabraham/flashpca) | [Link](https://anaconda.org/dnachun/r-flashpcar) | flashpcar | 2.1 | dnachun | GPL‑3.0‑or‑later | -| r-gridextra | [Link](https://cran.r-project.org/web/packages/gridExtra/index.html) | [Link](https://anaconda.org/conda-forge/r-gridextra) | flashpcar | 2.3 | conda‑forge | GPL‑2.0‑or‑later | -| r-matrixstats | [Link](https://cran.rstudio.com/web/packages/matrixStats/index.html) | [Link](https://anaconda.org/conda-forge/r-matrixstats) | flashpcar | 1.0.0 | conda‑forge | Artistic‑2.0 | -| r-rlang | [Link](https://cran.r-project.org/web/packages/rlang/index.html) | [Link](https://anaconda.org/conda-forge/r-rlang) | flashpcar, factor_analysis | 1.1.1 | conda‑forge | GPL‑3.0‑only | -| hello | [Link](https://www.gnu.org/software/hello/) | [Link](https://anaconda.org/dnachun/hello) | hello | 2.12.1 | dnachun | GPL‑3.0‑or‑later | -| r-leafcutter | [Link](https://github.com/davidaknowles/leafcutter) | [Link](https://anaconda.org/dnachun/r-leafcutter) | leafcutter | 0.2.9 | dnachun | GPL‑3.0‑or‑later | -| regtools | [Link](https://github.com/griffithlab/regtools) | [Link](https://anaconda.org/bioconda/regtools) | leafcutter | 1.0.0 | bioconda | MIT | -| metal | [Link](https://github.com/statgen/METAL) | [Link](https://anaconda.org/dnachun/metal) | metal | 2020_05_05 | dnachun | BSD‑3‑Clause | -| bioconductor-illuminahumanmethylation450kmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylation450kmanifest) | methylation | 0.4.0 | bioconda | Artistic‑2.0 | -| bioconductor-illuminahumanmethylationepicmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylationepicmanifest) | methylation | 0.3.0 | bioconda | Artistic‑2.0 | -| bioconductor-limma | [Link](https://bioconductor.org/packages/release/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | methylation | 3.56.2 | bioconda | GPL‑2.0‑or‑later | -| bioconductor-minfi | [Link](https://bioconductor.org/packages/release/bioc/html/minfi.html) | [Link](https://anaconda.org/bioconda/bioconductor-minfi) | methylation | 1.46.0 | bioconda | Artistic‑2.0 | -| bioconductor-preprocesscore | [Link](https://bioconductor.org/packages/release/bioc/html/preprocessCore.html) | [Link](https://anaconda.org/bioconda/bioconductor-preprocesscore) | methylation | 1.62.1 | bioconda | LGPL‑2.0‑or‑later | -| bioconductor-sesame | [Link](https://www.bioconductor.org/packages/release/bioc/html/sesame.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesame) | methylation | 1.18.4 | bioconda | MIT AND Other | -| bioconductor-sesamedata | [Link](https://bioconductor.org/packages/release/data/experiment/html/sesameData.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesamedata) | methylation | 1.18.0 | bioconda | Artistic‑2.0 | -| r-glmnet | [Link](https://cran.r-project.org/web/packages/glmnet/index.html) | [Link](https://anaconda.org/r/r-glmnet) | methylation | 4.1 | conda‑forge | GPL‑2.0‑or‑later | -| r-data.table | [Link](https://cran.r-project.org/web/packages/data.table/index.html) | [Link](https://anaconda.org/conda-forge/r-data.table) | methylation, quantqtl | 1.14.8 | conda‑forge | MPL‑2.0 | -| bioconductor-biocsingular | [Link](https://bioconductor.org/packages/release/bioc/html/BiocSingular.html) | [Link](https://anaconda.org/bioconda/bioconductor-biocsingular) | pcatools | 1.16.0 | bioconda | GPL‑3.0‑or‑later | -| bioconductor-pcatools | [Link](https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html) | [Link](https://anaconda.org/bioconda/bioconductor-pcatools) | pcatools | 2.12.0 | bioconda | GPL‑3.0‑or‑later | -| r-rmtstat | [Link](https://cran.r-project.org/web/packages/RMTstat/index.html) | [Link](https://anaconda.org/conda-forge/r-rmtstat) | pcatools | 0.3.1 | conda‑forge | BSD‑3‑Clause | -| r-fsusier | [Link](https://github.com/stephenslab/fsusier) | [Link](https://anaconda.org/dnachun/r-fsusier) | pecotmr | 0.2.0 | dnachun | GPL‑3.0‑or‑later | -| r-mvsusier | [Link](https://github.com/stephenslab/mvsusieR) | [Link](https://anaconda.org/dnachun/r-mvsusier) | pecotmr | 0.1.7 | dnachun | GPL‑3.0‑or‑later | -| r-pecotmr | [Link](https://github.com/cumc/pecotmr) | [Link](https://anaconda.org/dnachun/r-pecotmr) | pecotmr | 0.1.56 | dnachun | GPL‑3.0‑or‑later | -| r-susier | [Link](https://github.com/stephenslab/susieR) | [Link](https://anaconda.org/conda-forge/r-susier) | pecotmr, fastenloc | 0.14.7 | conda‑forge | MIT | -| backports.zoneinfo | [Link](https://pypi.org/project/backports.zoneinfo/) | [Link](https://anaconda.org/conda-forge/backports.zoneinfo) | pecotmr, quantqtl | 0.2.1 | conda‑forge | Apache‑2.0 | -| bioconductor-variantannotation | [Link](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) | [Link](https://anaconda.org/bioconda/bioconductor-variantannotation) | pecotmr, quantqtl | 1.48.1 | bioconda | Artistic‑2.0 | -| python-ldstore | [Link](https://pypi.org/project/ldstore/) | [Link](https://anaconda.org/dnachun/python-ldstore) | pecotmr, quantqtl | 0.1.9 | dnachun | MIT | -| r-complexupset | [Link](https://cran.r-project.org/web/packages/ComplexUpset/index.html) | [Link](https://anaconda.org/conda-forge/r-complexupset) | pecotmr, quantqtl | 1.3.3 | conda‑forge | MIT | -| r-cowplot | [Link](https://cran.r-project.org/web/packages/cowplot/index.html) | [Link](https://anaconda.org/conda-forge/r-cowplot) | pecotmr, quantqtl | 1.1.1 | conda‑forge | GPL‑2.0‑only | -| r-genio | [Link](https://cran.r-project.org/web/packages/genio/index.html) | [Link](https://anaconda.org/dnachun/r-genio) | pecotmr, quantqtl | 1.1.2 | dnachun | GPL‑3.0‑or‑later | -| r-gwasrapidd | [Link](https://cran.r-project.com/web/packages/gwasrapidd/index.html) | [Link](https://anaconda.org/dnachun/r-gwasrapidd) | pecotmr, quantqtl | 0.99.14 | dnachun | MIT | -| r-udr | [Link](https://github.com/stephenslab/udr) | [Link](https://anaconda.org/dnachun/r-udr) | pecotmr, quantqtl | 0.3.154 | dnachun | BSD‑3‑Clause | -| finemap | [Link](http://christianbenner.com) | [Link](https://anaconda.org/bioconda/finemap) | polyfun | 1.4.1 | bioconda | Other | -| ldstore | [Link](http://christianbenner.com) | [Link](https://anaconda.org/dnachun/ldstore) | polyfun | 2 | dnachun | Other | -| polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT | -| bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | -| suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | -| r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause | -| r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other | -| r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later | -| r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | GPL‑2.0‑or‑later | -| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | -| r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | -| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | -| ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | dnachun | Apache‑2.0 | -| r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | -| bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | -| bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | -| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | bioconda | GPL‑3.0‑or‑later | -| fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | -| fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | -| gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | -| gtex-pipeline-gene_model | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-gene_model) | rna_quantification | gtex_v8 | dnachun | Other | -| gtex-pipeline-qtl | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-qtl) | rna_quantification | gtex_v8 | dnachun | Other | -| gtex-pipeline-rnaseq | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) | [Link](https://anaconda.org/dnachun/gtex-pipeline-rnaseq) | rna_quantification | gtex_v8 | dnachun | Other | -| kallisto | [Link](https://github.com/pachterlab/kallisto) | [Link](https://anaconda.org/bioconda/kallisto) | rna_quantification | 0.50.0 | bioconda | BSD‑2‑Clause | -| kent-tools | [Link](https://genome.ucsc.edu/) | [Link](https://anaconda.org/dnachun/kent-tools) | rna_quantification | 438 | dnachun | MIT | -| multiqc | [Link](https://github.com/ewels/MultiQC) | [Link](https://anaconda.org/bioconda/multiqc) | rna_quantification | 1.15 | bioconda | GPL‑3.0‑or‑later | -| picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | -| pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | -| pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | -| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | -| rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | -| rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | -| star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11b | bioconda | GPL‑3.0‑or‑later | -| trimmomatic | [Link](https://github.com/timflutre/trimmomatic) | [Link](https://anaconda.org/bioconda/trimmomatic) | rna_quantification | 0.39 | bioconda | GPL‑3.0‑or‑later | -| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | rna_quantification, tensorqtl, quantqtl | 1.3.5 | conda‑forge | BSD‑3‑Clause | -| bioconductor-edger | [Link](https://bioconductor.org/packages/3.18/bioc/html/edgeR.html) | [Link](https://anaconda.org/bioconda/bioconductor-edger) | seurat | 4.0.2 | bioconda | GPL‑2.0‑or‑later | -| bioconductor-limma | [Link](https://bioconductor.org/packages/3.18/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | seurat | 3.58.1 | bioconda | GPL‑2.0‑or‑later | -| r-seurat | [Link](https://satijalab.org/seurat) | [Link](https://anaconda.org/conda-forge/r-seurat) | seurat | 5.0.1 | conda‑forge | MIT | -| bioconductor-qvalue | [Link](https://www.bioconductor.org/packages/release/bioc/html/qvalue.html) | [Link](https://anaconda.org/bioconda/bioconductor-qvalue) | tensorqtl | 2.32.0 | bioconda | LGPL‑3.0‑or‑later | -| multipy | [Link](https://github.com/puolival/multipy) | [Link](https://anaconda.org/dnachun/multipy) | tensorqtl | 0.16 | dnachun | BSD‑3‑Clause | -| qvalue | [Link](https://pypi.org/project/qvalue/) | [Link](https://anaconda.org/dnachun/qvalue) | tensorqtl | 0.1.3 | bioconda | BSD‑3‑Clause | -| tensorqtl | [Link](https://github.com/broadinstitute/tensorqtl) | [Link](https://anaconda.org/dnachun/tensorqtl) | tensorqtl | 1.0.8 | dnachun | BSD‑3‑Clause | -| altair | [Link](https://pypi.org/project/altair/) | [Link](https://anaconda.org/conda-forge/altair) | universal | | conda‑forge | BSD‑3‑Clause | -| awscli | [Link](https://github.com/aws/aws-cli) | [Link](https://anaconda.org/conda-forge/awscli) | universal | | conda‑forge | Apache‑2.0 | -| bash_kernel | [Link](https://github.com/takluyver/bash_kernel) | [Link](https://anaconda.org/conda-forge/bash_kernel) | universal | | conda‑forge | BSD‑3‑Clause | -| feather-format | [Link](https://pypi.org/project/feather-format/) | [Link](https://anaconda.org/conda-forge/feather-format) | universal | | conda‑forge | Apache‑2.0 | -| formulaic | [Link](https://github.com/matthewwardrop/formulaic) | [Link](https://anaconda.org/conda-forge/formulaic) | universal | | conda‑forge | MIT | -| imageio | [Link](https://pypi.org/project/imageio/) | [Link](https://anaconda.org/conda-forge/imageio) | universal | | conda‑forge | BSD‑2‑Clause | -| ipykernel | [Link](https://pypi.org/project/ipykernel/) | [Link](https://anaconda.org/conda-forge/ipykernel) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyter_contrib_nbextensions | [Link](https://pypi.org/project/jupyter-contrib-nbextensions/) | [Link](https://anaconda.org/conda-forge/jupyter_contrib_nbextensions) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyterlab | [Link](https://pypi.org/project/jupyterlab/) | [Link](https://anaconda.org/conda-forge/jupyterlab) | universal | | conda‑forge | BSD‑3‑Clause | -| jupyterlab-sos | [Link](https://pypi.org/project/jupyterlab-sos/) | [Link](https://anaconda.org/conda-forge/jupyterlab-sos) | universal | | conda‑forge | BSD‑3‑Clause | -| markdown-kernel | [Link](https://pypi.org/project/markdown-kernel/) | [Link](https://anaconda.org/conda-forge/markdown-kernel) | universal | | conda‑forge | BSD‑3‑Clause | -| matplotlib | [Link](https://pypi.org/project/matplotlib/) | [Link](https://anaconda.org/conda-forge/matplotlib) | universal | | conda‑forge | PSF‑2.0 AND CC0‑1.0 | -| nbdime | [Link](https://pypi.org/project/nbdime/) | [Link](https://anaconda.org/conda-forge/nbdime) | universal | | conda‑forge | BSD‑3‑Clause | -| notebook | [Link](https://pypi.org/project/notebook/) | [Link](https://anaconda.org/conda-forge/notebook) | universal | | conda‑forge | BSD‑3‑Clause | -| numpy | [Link](https://pypi.org/project/numpy/) | [Link](https://anaconda.org/conda-forge/numpy) | universal | | conda‑forge | BSD‑3‑Clause | -| openpyxl | [Link](https://pypi.org/project/openpyxl/) | [Link](https://anaconda.org/conda-forge/openpyxl) | universal | | conda‑forge | MIT | -| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | universal | | conda‑forge | BSD‑3‑Clause | -| parallel | [Link](https://www.gnu.org/software/parallel/) | [Link](https://anaconda.org/conda-forge/parallel) | universal | | conda‑forge | GPL‑3.0‑or‑later | -| plotnine | [Link](https://pypi.org/project/plotnine/) | [Link](https://anaconda.org/conda-forge/plotnine) | universal | | conda‑forge | MIT | -| ptpython | [Link](https://pypi.org/project/ptpython/) | [Link](https://anaconda.org/conda-forge/ptpython) | universal | | conda‑forge | BSD‑3‑Clause | -| pytables | [Link](https://pypi.org/project/tables/) | [Link](https://anaconda.org/conda-forge/pytables) | universal | | conda‑forge | BSD‑3‑Clause | -| r-irkernel | [Link](https://cran.rstudio.com/web/packages/IRkernel/index.html) | [Link](https://anaconda.org/conda-forge/r-irkernel) | universal | | conda‑forge | MIT | -| r-languageserver | [Link](https://cran.r-project.org/web/packages/languageserver/index.html) | [Link](https://anaconda.org/search?q=r-languageserver) | universal | | conda‑forge | MIT | -| r-tidyverse | [Link](https://cran.r-project.org/web/packages/tidyverse/index.html) | [Link](https://anaconda.org/conda-forge/r-tidyverse) | universal | | conda‑forge | MIT | -| rpy2 | [Link](https://pypi.org/project/rpy2/) | [Link](https://anaconda.org/conda-forge/rpy2) | universal | | conda‑forge | GPL‑2.0‑or‑later | -| scikit-learn | [Link](https://pypi.org/project/scikit-learn/) | [Link](https://anaconda.org/conda-forge/scikit-learn) | universal | | conda‑forge | BSD‑3‑Clause | -| scipy | [Link](https://pypi.org/project/scipy/) | [Link](https://anaconda.org/conda-forge/scipy) | universal | | conda‑forge | BSD‑3‑Clause | -| seaborn | [Link](https://pypi.org/project/seaborn/) | [Link](https://anaconda.org/conda-forge/seaborn) | universal | | conda‑forge | BSD‑3‑Clause | -| sos | [Link](https://pypi.org/project/sos/) | [Link](https://anaconda.org/conda-forge/sos) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-bash | [Link](https://pypi.org/project/sos-bash/) | [Link](https://anaconda.org/conda-forge/sos-bash) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-notebook | [Link](https://pypi.org/project/sos-notebook/) | [Link](https://anaconda.org/conda-forge/sos-notebook) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-pbs | [Link](https://pypi.org/project/sos-pbs/) | [Link](https://anaconda.org/conda-forge/sos-pbs) | universal | | conda‑forge | BSD‑3‑Clause | -| sos-python | [Link](https://pypi.org/project/sos-python/) | [Link](https://anaconda.org/conda-forge/sos-python) | universal | | conda‑forge | BSD‑3‑Clause | -| statsmodels | [Link](https://pypi.org/project/statsmodels/) | [Link](https://anaconda.org/conda-forge/statsmodels) | universal | | conda‑forge | BSD‑3‑Clause | -| wand | [Link](https://pypi.org/project/wand/) | [Link](https://anaconda.org/conda-forge/wand) | universal | | conda‑forge | BSD‑3‑Clause | \ No newline at end of file +| Package | Homepage | Conda package | Environment | Version | Channel | License | +|:--------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------|:-----------|:-------------------|:---------------------------------------| +| apex | [Link](https://github.com/corbinq/apex) | [Link](https://anaconda.org/dnachun/apex) | apex | 0.2-alpha | dnachun | Other | +| htslib | [Link](http://www.htslib.org/) | [Link](https://anaconda.org/bioconda/htslib) | apex, factor_analysis, bioinfo, methylation, pcatools, pecotmr, quantqtl, tensorqtl, rna_quantification | | bioconda | MIT | +| gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | +| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | bioinfo | 2.3.0 | dnachun | GPL‑3.0‑or‑later | +| plink | [Link](https://www.cog-genomics.org/plink2) | [Link](https://anaconda.org/bioconda/plink) | bioinfo | 1.90b6.21 | bioconda | GPL‑3.0‑or‑later | +| plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | +| qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | +| r-bedtoolsr | [Link](https://github.com/PhanstielLab/bedtoolsr) | [Link](https://anaconda.org/bioconda/r-bedtoolsr) | bioinfo | 2.30.0.2 | bioconda | MIT | +| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | +| r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | +| snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | +| snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | +| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL‑3.0‑or‑later | +| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other | +| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT | +| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL‑2.0‑only | +| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL‑3.0‑or‑later | +| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later | +| r-missforest | [Link](https://github.com/stekhoven/missForest) | [Link](https://anaconda.org/conda-forge/r-missforest) | factor_analysis | 1.5 | conda‑forge | GPL‑2.0‑or‑later | +| r-rcppeigen | [Link](https://cran.r-project.org/web/packages/RcppEigen/index.html) | [Link](https://anaconda.org/conda-forge/r-rcppeigen) | factor_analysis | 0.3.3.9.3 | conda‑forge | GPL‑2.0‑or‑later | +| r-snow | [Link](https://github.com/cran/snow) | [Link](https://anaconda.org/conda-forge/r-snow) | factor_analysis | 0.4_4 | conda‑forge | GPL‑2.0‑only | +| r-softimpute | [Link](https://github.com/cran/softImpute) | [Link](https://anaconda.org/conda-forge/r-softimpute) | factor_analysis | 1.4_1 | conda‑forge | GPL‑2.0‑only | +| dap-g | [Link](https://github.com/xqwen/dap) | [Link](https://anaconda.org/dnachun/dap-g) | fastenloc | 1.0.0 | dnachun | AGPL‑3.0‑or‑later | +| fastenloc | [Link](https://github.com/xqwen/fastenloc) | [Link](https://anaconda.org/dnachun/fastenloc) | fastenloc | 2 | dnachun | GPL‑3.0‑or‑later | +| torus | [Link](https://github.com/xqwen/torus) | [Link](https://anaconda.org/dnachun/torus) | fastenloc | 1 | dnachun | Other | +| r-flashpcar | [Link](https://github.com/gabraham/flashpca) | [Link](https://anaconda.org/dnachun/r-flashpcar) | flashpcar | 2.1 | dnachun | GPL‑3.0‑or‑later | +| r-gridextra | [Link](https://cran.r-project.org/web/packages/gridExtra/index.html) | [Link](https://anaconda.org/conda-forge/r-gridextra) | flashpcar | 2.3 | conda‑forge | GPL‑2.0‑or‑later | +| r-matrixstats | [Link](https://cran.rstudio.com/web/packages/matrixStats/index.html) | [Link](https://anaconda.org/conda-forge/r-matrixstats) | flashpcar | 1.0.0 | conda‑forge | Artistic‑2.0 | +| r-rlang | [Link](https://cran.r-project.org/web/packages/rlang/index.html) | [Link](https://anaconda.org/conda-forge/r-rlang) | flashpcar, factor_analysis | 1.1.1 | conda‑forge | GPL‑3.0‑only | +| hello | [Link](https://www.gnu.org/software/hello/) | [Link](https://anaconda.org/dnachun/hello) | hello | 2.12.1 | dnachun | GPL‑3.0‑or‑later | +| r-leafcutter | [Link](https://github.com/davidaknowles/leafcutter) | [Link](https://anaconda.org/dnachun/r-leafcutter) | leafcutter | 0.2.9 | dnachun | GPL‑3.0‑or‑later | +| regtools | [Link](https://github.com/griffithlab/regtools) | [Link](https://anaconda.org/bioconda/regtools) | leafcutter | 1.0.0 | bioconda | MIT | +| metal | [Link](https://github.com/statgen/METAL) | [Link](https://anaconda.org/dnachun/metal) | metal | 2020_05_05 | dnachun | BSD‑3‑Clause | +| bioconductor-illuminahumanmethylation450kmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylation450kmanifest) | methylation | 0.4.0 | bioconda | Artistic‑2.0 | +| bioconductor-illuminahumanmethylationepicmanifest | [Link](https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICmanifest.html) | [Link](https://anaconda.org/bioconda/bioconductor-illuminahumanmethylationepicmanifest) | methylation | 0.3.0 | bioconda | Artistic‑2.0 | +| bioconductor-limma | [Link](https://bioconductor.org/packages/release/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | methylation | 3.56.2 | bioconda | GPL‑2.0‑or‑later | +| bioconductor-minfi | [Link](https://bioconductor.org/packages/release/bioc/html/minfi.html) | [Link](https://anaconda.org/bioconda/bioconductor-minfi) | methylation | 1.46.0 | bioconda | Artistic‑2.0 | +| bioconductor-preprocesscore | [Link](https://bioconductor.org/packages/release/bioc/html/preprocessCore.html) | [Link](https://anaconda.org/bioconda/bioconductor-preprocesscore) | methylation | 1.62.1 | bioconda | LGPL‑2.0‑or‑later | +| bioconductor-sesame | [Link](https://www.bioconductor.org/packages/release/bioc/html/sesame.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesame) | methylation | 1.18.4 | bioconda | MIT AND Other | +| bioconductor-sesamedata | [Link](https://bioconductor.org/packages/release/data/experiment/html/sesameData.html) | [Link](https://anaconda.org/bioconda/bioconductor-sesamedata) | methylation | 1.18.0 | bioconda | Artistic‑2.0 | +| r-glmnet | [Link](https://cran.r-project.org/web/packages/glmnet/index.html) | [Link](https://anaconda.org/r/r-glmnet) | methylation | 4.1 | conda‑forge | GPL‑2.0‑or‑later | +| r-data.table | [Link](https://cran.r-project.org/web/packages/data.table/index.html) | [Link](https://anaconda.org/conda-forge/r-data.table) | methylation, quantqtl | 1.14.8 | conda‑forge | MPL‑2.0 | +| bioconductor-biocsingular | [Link](https://bioconductor.org/packages/release/bioc/html/BiocSingular.html) | [Link](https://anaconda.org/bioconda/bioconductor-biocsingular) | pcatools | 1.16.0 | bioconda | GPL‑3.0‑or‑later | +| bioconductor-pcatools | [Link](https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html) | [Link](https://anaconda.org/bioconda/bioconductor-pcatools) | pcatools | 2.12.0 | bioconda | GPL‑3.0‑or‑later | +| r-rmtstat | [Link](https://cran.r-project.org/web/packages/RMTstat/index.html) | [Link](https://anaconda.org/conda-forge/r-rmtstat) | pcatools | 0.3.1 | conda‑forge | BSD‑3‑Clause | +| r-fsusier | [Link](https://github.com/stephenslab/fsusier) | [Link](https://anaconda.org/dnachun/r-fsusier) | pecotmr | 0.2.0 | dnachun | GPL‑3.0‑or‑later | +| r-mvsusier | [Link](https://github.com/stephenslab/mvsusieR) | [Link](https://anaconda.org/dnachun/r-mvsusier) | pecotmr | 0.1.7 | dnachun | GPL‑3.0‑or‑later | +| r-pecotmr | [Link](https://github.com/cumc/pecotmr) | [Link](https://anaconda.org/dnachun/r-pecotmr) | pecotmr | 0.1.56 | dnachun | GPL‑3.0‑or‑later | +| r-susier | [Link](https://github.com/stephenslab/susieR) | [Link](https://anaconda.org/conda-forge/r-susier) | pecotmr, fastenloc | 0.14.7 | conda‑forge | MIT | +| backports.zoneinfo | [Link](https://pypi.org/project/backports.zoneinfo/) | [Link](https://anaconda.org/conda-forge/backports.zoneinfo) | pecotmr, quantqtl | 0.2.1 | conda‑forge | Apache‑2.0 | +| bioconductor-variantannotation | [Link](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) | [Link](https://anaconda.org/bioconda/bioconductor-variantannotation) | pecotmr, quantqtl | 1.48.1 | bioconda | Artistic‑2.0 | +| python-ldstore | [Link](https://pypi.org/project/ldstore/) | [Link](https://anaconda.org/dnachun/python-ldstore) | pecotmr, quantqtl | 0.1.9 | dnachun | MIT | +| r-complexupset | [Link](https://cran.r-project.org/web/packages/ComplexUpset/index.html) | [Link](https://anaconda.org/conda-forge/r-complexupset) | pecotmr, quantqtl | 1.3.3 | conda‑forge | MIT | +| r-cowplot | [Link](https://cran.r-project.org/web/packages/cowplot/index.html) | [Link](https://anaconda.org/conda-forge/r-cowplot) | pecotmr, quantqtl | 1.1.1 | conda‑forge | GPL‑2.0‑only | +| r-genio | [Link](https://cran.r-project.org/web/packages/genio/index.html) | [Link](https://anaconda.org/dnachun/r-genio) | pecotmr, quantqtl | 1.1.2 | dnachun | GPL‑3.0‑or‑later | +| r-gwasrapidd | [Link](https://cran.r-project.com/web/packages/gwasrapidd/index.html) | [Link](https://anaconda.org/dnachun/r-gwasrapidd) | pecotmr, quantqtl | 0.99.14 | dnachun | MIT | +| r-udr | [Link](https://github.com/stephenslab/udr) | [Link](https://anaconda.org/dnachun/r-udr) | pecotmr, quantqtl | 0.3.154 | dnachun | BSD‑3‑Clause | +| finemap | [Link](http://christianbenner.com) | [Link](https://anaconda.org/bioconda/finemap) | polyfun | 1.4.1 | bioconda | Other | +| ldstore | [Link](http://christianbenner.com) | [Link](https://anaconda.org/dnachun/ldstore) | polyfun | 2 | dnachun | Other | +| polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT | +| bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | +| suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | +| r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause | +| r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other | +| r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later | +| r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | GPL‑2.0‑or‑later | +| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | +| r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | +| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | +| ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | dnachun | Apache‑2.0 | +| r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | +| bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | +| bedtools | [Link](https://github.com/arq5x/bedtools2) | [Link](https://anaconda.org/bioconda/bedtools) | rna_quantification | 2.31.0 | bioconda | MIT | +| deeptools | [Link](https://github.com/deeptools/deepTools) | [Link](https://anaconda.org/bioconda/deeptools) | rna_quantification | 3.5.4 | bioconda | GPL‑3.0‑or‑later | +| fastp | [Link](https://github.com/OpenGene/fastp) | [Link](https://anaconda.org/bioconda/fastp) | rna_quantification | 0.23.4 | bioconda | MIT | +| fastqc | [Link](https://github.com/s-andrews/FastQC) | [Link](https://anaconda.org/bioconda/fastqc) | rna_quantification | 0.12.1 | bioconda | GPL‑3.0‑or‑later | +| gffread | [Link](https://github.com/gpertea/gffread) | [Link](https://anaconda.org/bioconda/gffread) | rna_quantification | 0.12.7 | bioconda | MIT | +| gtex-pipeline-gene_model | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-gene_model) | rna_quantification | gtex_v8 | dnachun | Other | +| gtex-pipeline-qtl | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) | [Link](https://anaconda.org/dnachun/gtex-pipeline-qtl) | rna_quantification | gtex_v8 | dnachun | Other | +| gtex-pipeline-rnaseq | [Link](https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) | [Link](https://anaconda.org/dnachun/gtex-pipeline-rnaseq) | rna_quantification | gtex_v8 | dnachun | Other | +| kallisto | [Link](https://github.com/pachterlab/kallisto) | [Link](https://anaconda.org/bioconda/kallisto) | rna_quantification | 0.50.0 | bioconda | BSD‑2‑Clause | +| kent-tools | [Link](https://genome.ucsc.edu/) | [Link](https://anaconda.org/dnachun/kent-tools) | rna_quantification | 438 | dnachun | MIT | +| multiqc | [Link](https://github.com/ewels/MultiQC) | [Link](https://anaconda.org/bioconda/multiqc) | rna_quantification | 1.15 | bioconda | GPL‑3.0‑or‑later | +| picard | [Link](https://github.com/broadinstitute/picard) | [Link](https://anaconda.org/bioconda/picard) | rna_quantification | 3.1.0 | bioconda | MIT | +| pyarrow | [Link](https://pypi.org/project/pyarrow/) | [Link](https://anaconda.org/conda-forge/pyarrow) | rna_quantification | 13.0.0 | conda‑forge | Apache‑2.0 | +| pybigwig | [Link](https://pypi.org/project/pyBigWig/) | [Link](https://anaconda.org/bioconda/pybigwig) | rna_quantification | 0.3.22 | bioconda | MIT | +| r-ape | [Link](https://github.com/emmanuelparadis/ape) | [Link](https://anaconda.org/conda-forge/r-ape) | rna_quantification | 5.7 | conda‑forge | GPL‑3.0‑or‑later | +| rnaseqc | [Link](https://github.com/getzlab/rnaseqc) | [Link](https://anaconda.org/dnachun/rnaseqc) | rna_quantification | 2.4.2 | dnachun | BSD‑3‑Clause | +| rsem | [Link](https://github.com/deweylab/RSEM) | [Link](https://anaconda.org/bioconda/rsem) | rna_quantification | 1.3.3 | bioconda | GPL‑3.0‑or‑later | +| star | [Link](https://github.com/alexdobin/STAR) | [Link](https://anaconda.org/bioconda/star) | rna_quantification | 2.7.11b | bioconda | GPL‑3.0‑or‑later | +| trimmomatic | [Link](https://github.com/timflutre/trimmomatic) | [Link](https://anaconda.org/bioconda/trimmomatic) | rna_quantification | 0.39 | bioconda | GPL‑3.0‑or‑later | +| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | rna_quantification, tensorqtl, quantqtl | 1.3.5 | conda‑forge | BSD‑3‑Clause | +| bioconductor-edger | [Link](https://bioconductor.org/packages/3.18/bioc/html/edgeR.html) | [Link](https://anaconda.org/bioconda/bioconductor-edger) | seurat | 4.0.2 | bioconda | GPL‑2.0‑or‑later | +| bioconductor-limma | [Link](https://bioconductor.org/packages/3.18/bioc/html/limma.html) | [Link](https://anaconda.org/bioconda/bioconductor-limma) | seurat | 3.58.1 | bioconda | GPL‑2.0‑or‑later | +| r-seurat | [Link](https://satijalab.org/seurat) | [Link](https://anaconda.org/conda-forge/r-seurat) | seurat | 5.0.1 | conda‑forge | MIT | +| bioconductor-qvalue | [Link](https://www.bioconductor.org/packages/release/bioc/html/qvalue.html) | [Link](https://anaconda.org/bioconda/bioconductor-qvalue) | tensorqtl | 2.32.0 | bioconda | LGPL‑3.0‑or‑later | +| multipy | [Link](https://github.com/puolival/multipy) | [Link](https://anaconda.org/dnachun/multipy) | tensorqtl | 0.16 | dnachun | BSD‑3‑Clause | +| qvalue | [Link](https://pypi.org/project/qvalue/) | [Link](https://anaconda.org/dnachun/qvalue) | tensorqtl | 0.1.3 | bioconda | BSD‑3‑Clause | +| tensorqtl | [Link](https://github.com/broadinstitute/tensorqtl) | [Link](https://anaconda.org/dnachun/tensorqtl) | tensorqtl | 1.0.8 | dnachun | BSD‑3‑Clause | +| altair | [Link](https://pypi.org/project/altair/) | [Link](https://anaconda.org/conda-forge/altair) | universal | | conda‑forge | BSD‑3‑Clause | +| awscli | [Link](https://github.com/aws/aws-cli) | [Link](https://anaconda.org/conda-forge/awscli) | universal | | conda‑forge | Apache‑2.0 | +| bash_kernel | [Link](https://github.com/takluyver/bash_kernel) | [Link](https://anaconda.org/conda-forge/bash_kernel) | universal | | conda‑forge | BSD‑3‑Clause | +| feather-format | [Link](https://pypi.org/project/feather-format/) | [Link](https://anaconda.org/conda-forge/feather-format) | universal | | conda‑forge | Apache‑2.0 | +| formulaic | [Link](https://github.com/matthewwardrop/formulaic) | [Link](https://anaconda.org/conda-forge/formulaic) | universal | | conda‑forge | MIT | +| imageio | [Link](https://pypi.org/project/imageio/) | [Link](https://anaconda.org/conda-forge/imageio) | universal | | conda‑forge | BSD‑2‑Clause | +| ipykernel | [Link](https://pypi.org/project/ipykernel/) | [Link](https://anaconda.org/conda-forge/ipykernel) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyter_contrib_nbextensions | [Link](https://pypi.org/project/jupyter-contrib-nbextensions/) | [Link](https://anaconda.org/conda-forge/jupyter_contrib_nbextensions) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyterlab | [Link](https://pypi.org/project/jupyterlab/) | [Link](https://anaconda.org/conda-forge/jupyterlab) | universal | | conda‑forge | BSD‑3‑Clause | +| jupyterlab-sos | [Link](https://pypi.org/project/jupyterlab-sos/) | [Link](https://anaconda.org/conda-forge/jupyterlab-sos) | universal | | conda‑forge | BSD‑3‑Clause | +| markdown-kernel | [Link](https://pypi.org/project/markdown-kernel/) | [Link](https://anaconda.org/conda-forge/markdown-kernel) | universal | | conda‑forge | BSD‑3‑Clause | +| matplotlib | [Link](https://pypi.org/project/matplotlib/) | [Link](https://anaconda.org/conda-forge/matplotlib) | universal | | conda‑forge | PSF‑2.0 AND CC0‑1.0 | +| nbdime | [Link](https://pypi.org/project/nbdime/) | [Link](https://anaconda.org/conda-forge/nbdime) | universal | | conda‑forge | BSD‑3‑Clause | +| notebook | [Link](https://pypi.org/project/notebook/) | [Link](https://anaconda.org/conda-forge/notebook) | universal | | conda‑forge | BSD‑3‑Clause | +| numpy | [Link](https://pypi.org/project/numpy/) | [Link](https://anaconda.org/conda-forge/numpy) | universal | | conda‑forge | BSD‑3‑Clause | +| openpyxl | [Link](https://pypi.org/project/openpyxl/) | [Link](https://anaconda.org/conda-forge/openpyxl) | universal | | conda‑forge | MIT | +| pandas | [Link](https://pypi.org/project/pandas/) | [Link](https://anaconda.org/conda-forge/pandas) | universal | | conda‑forge | BSD‑3‑Clause | +| parallel | [Link](https://www.gnu.org/software/parallel/) | [Link](https://anaconda.org/conda-forge/parallel) | universal | | conda‑forge | GPL‑3.0‑or‑later | +| plotnine | [Link](https://pypi.org/project/plotnine/) | [Link](https://anaconda.org/conda-forge/plotnine) | universal | | conda‑forge | MIT | +| ptpython | [Link](https://pypi.org/project/ptpython/) | [Link](https://anaconda.org/conda-forge/ptpython) | universal | | conda‑forge | BSD‑3‑Clause | +| pytables | [Link](https://pypi.org/project/tables/) | [Link](https://anaconda.org/conda-forge/pytables) | universal | | conda‑forge | BSD‑3‑Clause | +| r-irkernel | [Link](https://cran.rstudio.com/web/packages/IRkernel/index.html) | [Link](https://anaconda.org/conda-forge/r-irkernel) | universal | | conda‑forge | MIT | +| r-languageserver | [Link](https://cran.r-project.org/web/packages/languageserver/index.html) | [Link](https://anaconda.org/search?q=r-languageserver) | universal | | conda‑forge | MIT | +| r-tidyverse | [Link](https://cran.r-project.org/web/packages/tidyverse/index.html) | [Link](https://anaconda.org/conda-forge/r-tidyverse) | universal | | conda‑forge | MIT | +| rpy2 | [Link](https://pypi.org/project/rpy2/) | [Link](https://anaconda.org/conda-forge/rpy2) | universal | | conda‑forge | GPL‑2.0‑or‑later | +| scikit-learn | [Link](https://pypi.org/project/scikit-learn/) | [Link](https://anaconda.org/conda-forge/scikit-learn) | universal | | conda‑forge | BSD‑3‑Clause | +| scipy | [Link](https://pypi.org/project/scipy/) | [Link](https://anaconda.org/conda-forge/scipy) | universal | | conda‑forge | BSD‑3‑Clause | +| seaborn | [Link](https://pypi.org/project/seaborn/) | [Link](https://anaconda.org/conda-forge/seaborn) | universal | | conda‑forge | BSD‑3‑Clause | +| sos | [Link](https://pypi.org/project/sos/) | [Link](https://anaconda.org/conda-forge/sos) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-bash | [Link](https://pypi.org/project/sos-bash/) | [Link](https://anaconda.org/conda-forge/sos-bash) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-notebook | [Link](https://pypi.org/project/sos-notebook/) | [Link](https://anaconda.org/conda-forge/sos-notebook) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-pbs | [Link](https://pypi.org/project/sos-pbs/) | [Link](https://anaconda.org/conda-forge/sos-pbs) | universal | | conda‑forge | BSD‑3‑Clause | +| sos-python | [Link](https://pypi.org/project/sos-python/) | [Link](https://anaconda.org/conda-forge/sos-python) | universal | | conda‑forge | BSD‑3‑Clause | +| statsmodels | [Link](https://pypi.org/project/statsmodels/) | [Link](https://anaconda.org/conda-forge/statsmodels) | universal | | conda‑forge | BSD‑3‑Clause | +| wand | [Link](https://pypi.org/project/wand/) | [Link](https://anaconda.org/conda-forge/wand) | universal | | conda‑forge | BSD‑3‑Clause | \ No newline at end of file diff --git a/container/rna_quantification/rna_quantification.yml b/container/rna_quantification/rna_quantification.yml index 30b8bb6c..eedf3dcf 100644 --- a/container/rna_quantification/rna_quantification.yml +++ b/container/rna_quantification/rna_quantification.yml @@ -14,6 +14,7 @@ dependencies: - gtex-pipeline-gene_model=gtex_v8 - gtex-pipeline-qtl=gtex_v8 - gtex-pipeline-rnaseq=gtex_v8 + - htslib - kallisto=0.50.0 - kent-tools=438 - multiqc=1.15