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  • bioinfo
  • ngs_tools
  • Issues

  • Open 3
  • Closed 34
  • All 37
New issue
  • Priority Created date Last updated Milestone due date Due date Popularity Label priority Manual Title
  • 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
  • export TPM instead of FPKM tables
    #14 · created May 19, 2017 by brandl   rna_seq
    • CLOSED
    • 1
    updated Jun 19, 2017
  • 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
  • make sure that exported tables contain double-normalized counts and not just size-normalized ones
    #1 · created Feb 05, 2016 by brandl   rna_seq
    • CLOSED
    • 2
    updated Feb 12, 2019
  • 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
  • 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
  • dge_workflow: echoing R code in to Rscript not loading personal library packages
    #56 · created Jun 19, 2019 by domingue   rna_seq
    • CLOSED
    • 2
    updated Jun 20, 2019
  • dge workflow: add GTF an argument for differential gene expression
    #57 · created Jun 20, 2019 by domingue   rna_seq
    • 2
    updated Jun 28, 2019
  • expression_explorer: harcoded Rscipt path
    #67 · created Aug 15, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Aug 21, 2019
  • cut delimeter breaks fastqc_summary.R
    #70 · created Sep 09, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Sep 09, 2019
  • Grep error message crashes the script
    #71 · created Sep 09, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Sep 09, 2019
  • Changes in ggplot break boxplot in fastqc_summary.R
    #72 · created Sep 09, 2019 by domingue   rna_seq
    • CLOSED
    • 1
    updated Sep 09, 2019
  • Implement renvs
    #73 · created Sep 16, 2019 by domingue   mass_spec rna_seq
    • CLOSED
    • 2
    updated Feb 20, 2020
  • dge_workflow: fix lcf help
    #74 · created Oct 22, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Dec 02, 2019
  • dge_workflow: future improvements
    #75 · created Oct 22, 2019 by domingue   rna_seq
    • CLOSED
    • 1
    updated Jul 20, 2020
  • iGenome permissions
    #76 · created Nov 15, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Feb 20, 2020
  • dge _workflow: analyze duplicates has a broken link to the plot of the model (dupRadar)
    #81 · created Feb 10, 2020 by domingue   rna_seq
    • CLOSED
    • 1
    updated Feb 10, 2020
  • dge_workflow: collect_kallisto_data.R fails for paired-end data
    #84 · created Mar 12, 2020 by herseman   rna_seq
    • CLOSED
    • 2
    updated Mar 12, 2020
  • Hardcoded pvalue in plot
    #85 · created Mar 13, 2020 by domingue   rna_seq
    • CLOSED
    • 5
    updated Apr 15, 2020
  • Stranded counts
    #88 · created Mar 27, 2020 by domingue   rna_seq
    • 5
    updated Jul 13, 2020
  • argparser error when --bam_files is the last optional argument
    #90 · created Jul 01, 2020 by domingue   rna_seq
    • CLOSED
    • 4
    updated Jul 01, 2020
  • dge_workflow: expression_explorer app failed to load due to renamed/additional annotation columns
    #91 · created Jul 10, 2020 by herseman   rna_seq
    • CLOSED
    • 1
    updated Jul 10, 2020
  • GSEA
    #92 · created Aug 07, 2020 by domingue   rna_seq
    • CLOSED
    • 5
    updated Sep 23, 2020
  • GSEA: add option to use custom gene sets
    #93 · created Sep 09, 2020 by domingue   rna_seq
    • CLOSED
    • 1
    updated Sep 09, 2020
  • gsea: bug, hard-coded species
    #94 · created Sep 15, 2020 by domingue   rna_seq
    • CLOSED
    • 0
    updated Sep 15, 2020
  • gsea: bug, in extra sets the first line is being read as header
    #95 · created Sep 15, 2020 by domingue   rna_seq
    • CLOSED
    • 0
    updated Sep 15, 2020
  • gsea: generate results for each contrast
    #96 · created Sep 16, 2020 by domingue   rna_seq
    • CLOSED
    • 1
    updated Sep 23, 2020
  • gsea: improvments   2 of 4 tasks completed
    #97 · created Sep 24, 2020 by domingue   rna_seq
    • 0
    updated Oct 13, 2020
  • Gene enrichment: script selects random genes if list too large
    #98 · created Oct 07, 2020 by domingue   rna_seq
    • CLOSED
    • 2
    updated Oct 07, 2020
  • gsea: better description
    #99 · created Nov 12, 2020 by domingue   rna_seq
    • CLOSED
    • 2
    updated Nov 19, 2020
  • exDesign: numeric vs categorical variables and shrinkage method
    #100 · created Feb 15, 2021 by gohr   rna_seq
    • CLOSED
    • 0
    updated Feb 23, 2021
  • GSEA: improve color code of KEGG pathways
    #101 · created Mar 23, 2021 by gohr   rna_seq
    • CLOSED
    • 0
    updated Mar 23, 2021
  • gsea: improvement of description
    #102 · created Apr 08, 2021 by gohr   Bioinformatics Internal Non-rechargeable rna_seq
    • CLOSED
    • 1
    updated Apr 08, 2021
  • gsea: fixing expression explorer
    #103 · created Apr 08, 2021 by gohr   Bioinformatics Internal Non-rechargeable rna_seq
    • CLOSED
    • 0
    updated Apr 08, 2021