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ChIP-seq improvements #460

Merged
merged 20 commits into from
Sep 14, 2020
Merged

ChIP-seq improvements #460

merged 20 commits into from
Sep 14, 2020

Commits on Sep 17, 2019

  1. improving estimated fragment length

    @tovahmarkowitz
    tovahmarkowitz committed Sep 17, 2019
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Commits on Sep 23, 2019

  1. gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac… 

    …tiveDev
    @tovahmarkowitz
    tovahmarkowitz committed Sep 23, 2019
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  2. est fraglen; diffbind

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    tovahmarkowitz committed Sep 23, 2019
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Commits on Oct 28, 2019

  1. Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac… 

    …tiveDev
    @tovahmarkowitz
    tovahmarkowitz committed Oct 28, 2019
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  2. DiffBind and cleanup

    @tovahmarkowitz
    tovahmarkowitz committed Oct 28, 2019
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Commits on Nov 19, 2019

  1. Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac… 

    …tiveDev
    @tovahmarkowitz
    tovahmarkowitz committed Nov 19, 2019
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  2. ppqt changes

    @tovahmarkowitz
    tovahmarkowitz committed Nov 19, 2019
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Commits on Jan 6, 2020

  1. Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac… 

    …tiveDev
    @tovahmarkowitz
    tovahmarkowitz committed Jan 6, 2020
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  2. ppqt improvements and a few other details

    @tovahmarkowitz
    tovahmarkowitz committed Jan 6, 2020
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Commits on Apr 10, 2020

  1. 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 <[email protected]>
Co-authored-by: wong-nw <[email protected]>
Co-authored-by: jlac <[email protected]>

Co-authored-by: Skyler Kuhn <[email protected]>
Co-authored-by: Mayank  Tandon <[email protected]>
Co-authored-by: jlac <[email protected]>
Co-authored-by: skchronicles <[email protected]>
    @wong-nw @skchronicles
    @mtandon09 @jlac
    5 people authored Apr 10, 2020
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Commits on Apr 23, 2020

  1. improving ppqt, diffbind, frip, and jaccard

    @tovahmarkowitz
    tovahmarkowitz committed Apr 23, 2020
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  2. fixing merge issue

    @tovahmarkowitz
    tovahmarkowitz committed Apr 23, 2020
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Commits on May 8, 2020

  1. updating to most recent version of activeDev

    @tovahmarkowitz
    tovahmarkowitz committed May 8, 2020
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  2. fixed the InitialChIPseqQC.snakefile conflict

    @tovahmarkowitz
    tovahmarkowitz committed May 8, 2020
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Commits on May 10, 2020

  1. fastqc bug fixed

    @tovahmarkowitz
    tovahmarkowitz committed May 10, 2020
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  2. more memory for BWA in ChIP-seq pipeline

    @tovahmarkowitz
    tovahmarkowitz committed May 10, 2020
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Commits on Jun 17, 2020

  1. reverting ngsqc_plot to a version that functions

    @tovahmarkowitz
    tovahmarkowitz committed Jun 17, 2020
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Commits on Jun 23, 2020

  1. Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac… 

    …tiveDev
    @tovahmarkowitz
    tovahmarkowitz committed Jun 23, 2020
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  2. fixing FRiP

    @tovahmarkowitz
    tovahmarkowitz committed Jun 23, 2020
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Commits on Sep 14, 2020

  1. improved ChIP-seq PE and bug fixes

    @tovahmarkowitz
    tovahmarkowitz committed Sep 14, 2020
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