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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
  • sc_workflow: add script for the calculation of diffusion map and pseudo time using the `destiny` package
    #43 · created Mar 01, 2019 by herseman
    • CLOSED
    • 2
    updated Mar 05, 2019
  • sc_workflow: update sc_quality_check.R
    #42 · created Feb 28, 2019 by herseman
    • CLOSED
    • 4
    updated Mar 20, 2019
  • ms_workflow: ms_limma.R returns error when no differentially abundant proteins were found
    #41 · created Feb 14, 2019 by herseman   mass_spec
    • CLOSED
    • 1
    updated Feb 14, 2019
  • ms_workflow: handling of technical replicates
    #40 · created Feb 13, 2019 by herseman   mass_spec
    • 2
    updated Dec 09, 2019
  • general: create customized docker files for individual analyses done with our ngs_tools scripts
    #39 · created Feb 11, 2019 by herseman
    • 3
    updated Mar 14, 2019
  • general: save the actually used ngs_tools script in results data folder
    #38 · created Feb 11, 2019 by herseman
    • CLOSED
    • 7
    updated Mar 13, 2019
  • ms_workflow: handling of contaminations
    #37 · created Feb 08, 2019 by herseman   mass_spec
    • CLOSED
    • 1
    updated Dec 10, 2019
  • ms_workflow: add additional quality metrics to the differential abundance analysis output
    #36 · created Feb 06, 2019 by herseman   mass_spec
    • CLOSED
    • 3
    updated Mar 08, 2019
  • sc_workflow: write single script for Seurat workflow with tested and approved settings
    #35 · created Jan 16, 2019 by herseman
    • 3
    updated Mar 22, 2019
  • ms_workflow: report differential abundance proteins along with the identification type information as well as additional protein information
    #34 · created Jan 15, 2019 by herseman
    • CLOSED
    • 1
    updated Feb 01, 2019
  • 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: aggregate protein isoforms data on gene level
    #32 · created Jan 15, 2019 by herseman   mass_spec
    • 0
    updated Feb 08, 2019
  • ms_workflow: report number of peptides (unique and razor peptides) for each protein group
    #31 · created Jan 15, 2019 by herseman   mass_spec
    • 2
    updated Feb 08, 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
  • DESeq2 check current clustering method
    #24 · created Nov 15, 2017 by herseman
    • 0
    updated Nov 29, 2018
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