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Scrnaseq #437
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Scrnaseq #437
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skchronicles
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Apr 10, 2020
* 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>
skchronicles
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Apr 10, 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>
skchronicles
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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>
skchronicles
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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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