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  • bioinfo
  • ngs_tools
  • Issues

  • Open 15
  • Closed 88
  • All 103
New issue
  • Priority Created date Last updated Milestone due date Due date Popularity Label priority Manual Title
  • consider to use alpha for more correct p_adjustment
    #23 · created Nov 14, 2017 by brandl
    • CLOSED
    • 5
    updated May 14, 2020
  • write shiny app (results relative local app) for dge data
    #22 · created Nov 09, 2017 by herseman
    • CLOSED
    • 0
    updated Jan 19, 2018
  • run kallisto parallel to STAR
    #21 · created Nov 09, 2017 by herseman
    • 0
    updated Nov 09, 2017
  • report proportion of multi-mappers in STAR report
    #20 · created Nov 09, 2017 by herseman
    • 0
    updated Nov 16, 2017
  • use common q-score color scale for enrichment plots in cp_enrichment.R
    #19 · created Jul 19, 2017 by brandl
    • CLOSED
    • 0
    updated Nov 09, 2017
  • impl better means to access summary and quality statististcs
    #18 · created May 30, 2017 by brandl
    • CLOSED
    • 0
    updated Nov 09, 2017
  • better handling of outliers
    #17 · created May 30, 2017 by brandl
    • CLOSED
    • 0
    updated Mar 07, 2019
  • auto-detect strandedness when extracting count matrix
    #16 · created May 29, 2017 by brandl
    • CLOSED
    • 2
    updated Mar 27, 2020
  • try RNA-SeQC to get qc for bam files
    #15 · created May 19, 2017 by brandl
    • CLOSED
    • 1
    updated Dec 09, 2019
  • export TPM instead of FPKM tables
    #14 · created May 19, 2017 by brandl   rna_seq
    • CLOSED
    • 1
    updated Jun 19, 2017
  • Change bam_qc to report multi/single mapper proportions relative to number of aligned reads.
    #13 · created May 18, 2017 by brandl
    • CLOSED
    • 0
    updated Mar 07, 2019
  • Add option to perform diffex-test in mf_feat_counts.R using fc-cutoff > 0.
    #12 · created Apr 10, 2017 by brandl   rna_seq
    • CLOSED
    • 2
    updated Jun 19, 2017
  • Integrate tools to assess gc/3/5 bias, insert size, and capture efficiency
    #11 · created Oct 11, 2016 by brandl   rna_seq
    • CLOSED
    • 1
    updated Feb 20, 2020
  • use http://multiqc.info/ for qc reporting
    #10 · created Jul 29, 2016 by brandl   rna_seq
    • CLOSED
    • 1
    updated Nov 18, 2019
  • Export counts as TPM in featcounts_deseq_mf.R
    #9 · created May 18, 2016 by brandl   rna_seq
    • CLOSED
    • 0
    updated Jul 08, 2017
  • create tool to create igv session file list of bam files
    #8 · created May 14, 2016 by brandl   rna_seq
    • CLOSED
    • 1
    updated Jul 08, 2017
  • finish panther enrichment and reintegrate into cp_enrichment.R
    #7 · created May 12, 2016 by brandl   rna_seq
    • CLOSED
    • 2
    updated Feb 20, 2020
  • Add pcr duplication analysis for rna-seq workflow
    #6 · created Apr 22, 2016 by brandl   rna_seq
    • CLOSED
    • 0
    updated Nov 09, 2017
  • add frip statistic to cs-workflow
    #5 · created Mar 18, 2016 by brandl
    • CLOSED
    • 1
    updated Mar 07, 2019
  • Add groupGo to cp_enrichment
    #4 · created Mar 16, 2016 by brandl
    • CLOSED
    • 1
    updated Nov 09, 2017
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