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scRNASeq changes Feb 2020 #438
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* Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov>
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Apr 29, 2020
* scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
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Jun 17, 2020
* improving estimated fragment length * est fraglen; diffbind * DiffBind and cleanup * ppqt changes * ppqt improvements and a few other details * scRNASeq changes Feb 2020 (#438) * scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu> * improving ppqt, diffbind, frip, and jaccard * fixed the InitialChIPseqQC.snakefile conflict * fastqc bug fixed * more memory for BWA in ChIP-seq pipeline * reverting ngsqc_plot to a version that functions Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
skchronicles
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Sep 14, 2020
* improving estimated fragment length * est fraglen; diffbind * DiffBind and cleanup * ppqt changes * ppqt improvements and a few other details * scRNASeq changes Feb 2020 (#438) * scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu> * improving ppqt, diffbind, frip, and jaccard * fixed the InitialChIPseqQC.snakefile conflict * fastqc bug fixed * more memory for BWA in ChIP-seq pipeline * reverting ngsqc_plot to a version that functions * fixing FRiP * improved ChIP-seq PE and bug fixes Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
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ChangeLog Feb 2020
gui/scrnaseq.py
Add CITESeq dropdown menu for QC
Updated Differential Expression to include: choice of rds object for DE; Clustering resolutions to run DE on; which test to use for DE; min fraction; min fold change; change of groups and change of contrasts. Still needs to be tested thoroughly, but at the moment will not throw errors when running QC.
Rules/scrnaQC.snakefile
Move RMarkdown QC report from Scripts to QC to match expected snakefile output for rule qcReport_scrna
Add CITESeq parameter to rule qc_scrna
Add CITESeq parameter to rule integratedBbatch
Changed rule qc_scrna to use extension-free names from groups.tab file
scrnaQC.R
Add R libraries and fixed paths
Add catch to remove “.h5” from Sample IDs in Seurat object
Add multiple clustering resolutions
Add full SingleR outputs to misc meta.data
Corrected Immune Cell Expression to DICE
Add CITESeq read in and normalization/scaling
Correct indents for readability
Add Novershtern Hematopoeitic Data to human SingleR
integrateBatches.R
Add CITESeq renormalize and rescale
Add multiple clustering resolutions
Corrected loop for multiple clustering resolutions
Corrected output to contain single output RDS that matches snakemake output
Correct indents for readability
Correct clustering parameters call (dims.use -> dims, reduction.type -> reduction)
Added catch for large datasets. Default pcs to 50 if total sample size > 50k cells
cluster.json
Changed integratedBatch params to memory=200g, time=2 days
Changed qc_scrna params to memory=150g, time = 1 day
pipeliner2.py
Added mm10 to the included list for scRNASeq