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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
  • ms_workflow: report settings from MaxQuant log file
    #33 · created Jan 15, 2019 by herseman   mass_spec
    • CLOSED
    • 2
    updated Feb 12, 2019
  • ms_workflow: add option to run analysis on raw intensities instead of LFQs
    #30 · created Jan 15, 2019 by herseman
    • CLOSED
    • 0
    updated Jan 15, 2019
  • revise limma workflow for mass spec data
    #29 · created Jan 10, 2019 by herseman
    • CLOSED
    • 1
    updated Jan 11, 2019
  • ms_workflow: Improvemnts   7 of 9 tasks completed
    #28 · created Dec 07, 2018 by brandl   mass_spec
    • CLOSED
    • 3
    updated Dec 10, 2019
  • new ticket
    #27 · created Nov 15, 2018 by brandl   3h
    • CLOSED
    • 3
    updated Dec 07, 2018
  • update to more recent https://github.com/deeptools/deepTools/releases
    #26 · created Aug 16, 2018 by brandl   2h
    • CLOSED
    • 3
    updated Feb 20, 2020
  • report improvements
    #25 · created Nov 16, 2017 by brandl
    • CLOSED
    • 1
    updated Feb 20, 2020
  • 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
  • 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
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