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environment.yml
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environment.yml
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name: Sauron.v1
channels:
- conda-forge
- bioconda
- defaults
- anaconda
dependencies:
- r-base=3.5
- rstudio=1.1.456
- bioconductor-biomart=2.38
- bioconductor-flowpeaks=1.28
- bioconductor-genomeinfodbdata=1.2.0
- bioconductor-scater=1.10
- bioconductor-scran=1.10
- bioconductor-singlecellexperiment=1.4
- bioconductor-sva=3.30
# - bioconductor-slingshot=1.2.0
# - bioconductor-destiny=2.12.0
- bioconductor-monocle=2.10.0
- r-devtools=2.1.0
- r-biocmanager=1.30
- r-data.table=1.11
- r-dbscan=1.1
- r-dplyr=0.8
- r-fields=9.6
- r-igraph=1.2
- r-ineq=0.2
- r-optparse=1.6
- r-pheatmap=1.0
- r-rafalib=1.0
- r-rcolorbrewer=1.1
- r-scales=1.0
- r-seurat=3.0.1
- r-vegan=2.5
- r-venn=1.7
- r-hdf5r=1.2.0
- r-umap=0.2
- leidenalg=0.7.0
- umap-learn=0.3.7
- r-grr=0.9.5
- r-pbmcapply=1.4.1
- r-plot3d=1.1.1
- r-circlize
- r-wgcna
# - snakemake=5.5.4
# - r-raceid=0.1.3
- wget=1.19.4 # For compatibility with genomeinfodbdata (currently broken)