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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
  • 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
  • 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
  • export TPM instead of FPKM tables
    #14 · created May 19, 2017 by brandl   rna_seq
    • CLOSED
    • 1
    updated Jun 19, 2017
  • try RNA-SeQC to get qc for bam files
    #15 · created May 19, 2017 by brandl
    • CLOSED
    • 1
    updated Dec 09, 2019
  • auto-detect strandedness when extracting count matrix
    #16 · created May 29, 2017 by brandl
    • CLOSED
    • 2
    updated Mar 27, 2020
  • better handling of outliers
    #17 · created May 30, 2017 by brandl
    • CLOSED
    • 0
    updated Mar 07, 2019
  • impl better means to access summary and quality statististcs
    #18 · created May 30, 2017 by brandl
    • CLOSED
    • 0
    updated Nov 09, 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
  • couldn't export the bitr function in clusterprofiler
    #3 · created Mar 08, 2016 by lakshman
    • CLOSED
    • 6
    updated Jul 08, 2017
  • error in the plotDispEsts()
    #2 · created Mar 07, 2016 by lakshman
    • CLOSED
    • 7
    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
  • 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
  • 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
  • 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
  • report proportion of multi-mappers in STAR report
    #20 · created Nov 09, 2017 by herseman
    • 0
    updated Nov 16, 2017
  • run kallisto parallel to STAR
    #21 · created Nov 09, 2017 by herseman
    • 0
    updated Nov 09, 2017
  • write shiny app (results relative local app) for dge data
    #22 · created Nov 09, 2017 by herseman
    • CLOSED
    • 0
    updated Jan 19, 2018
  • consider to use alpha for more correct p_adjustment
    #23 · created Nov 14, 2017 by brandl
    • CLOSED
    • 5
    updated May 14, 2020
  • DESeq2 check current clustering method
    #24 · created Nov 15, 2017 by herseman
    • 0
    updated Nov 29, 2018
  • report improvements
    #25 · created Nov 16, 2017 by brandl
    • CLOSED
    • 1
    updated Feb 20, 2020
  • update to more recent https://github.com/deeptools/deepTools/releases
    #26 · created Aug 16, 2018 by brandl   2h
    • CLOSED
    • 3
    updated Feb 20, 2020
  • new ticket
    #27 · created Nov 15, 2018 by brandl   3h
    • CLOSED
    • 3
    updated Dec 07, 2018
  • ms_workflow: Improvemnts   7 of 9 tasks completed
    #28 · created Dec 07, 2018 by brandl   mass_spec
    • CLOSED
    • 3
    updated Dec 10, 2019
  • revise limma workflow for mass spec data
    #29 · created Jan 10, 2019 by herseman
    • CLOSED
    • 1
    updated Jan 11, 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
  • 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: aggregate protein isoforms data on gene level
    #32 · created Jan 15, 2019 by herseman   mass_spec
    • 0
    updated Feb 08, 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: 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
  • 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: 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
  • ms_workflow: handling of contaminations
    #37 · created Feb 08, 2019 by herseman   mass_spec
    • CLOSED
    • 1
    updated Dec 10, 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
  • 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
  • ms_workflow: handling of technical replicates
    #40 · created Feb 13, 2019 by herseman   mass_spec
    • 2
    updated Dec 09, 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
  • sc_workflow: update sc_quality_check.R
    #42 · created Feb 28, 2019 by herseman
    • CLOSED
    • 4
    updated Mar 20, 2019
  • 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: write ShinyApp to explore metrics from the initial quality control
    #44 · created Mar 04, 2019 by herseman
    • CLOSED
    • 3
    updated Mar 20, 2019
  • ms_workflow: move to peptide level
    #45 · created Mar 07, 2019 by herseman
    • 0
    updated Dec 10, 2019
  • sc_workflow: add additional gene information for the top50 most highly abundant features in `sc_quality_check.R`
    #46 · created Mar 13, 2019 by herseman
    • CLOSED
    • 1
    updated Mar 13, 2019
  • sc_workflow: add shinyApp to explore Seurat clusterings
    #47 · created Mar 20, 2019 by herseman
    • CLOSED
    • 5
    updated Mar 22, 2019
  • general: fix issues which occur due to updated R package versions
    #48 · created Apr 03, 2019 by herseman
    • CLOSED
    • 1
    updated Apr 09, 2019
  • general: create new human igenome for the Ensembl release 95
    #49 · created Apr 05, 2019 by herseman
    • CLOSED
    • 1
    updated Apr 05, 2019
  • general: create templates for R scripts and shinyApps and revise the dge_star_template
    #50 · created May 10, 2019 by herseman
    • 1
    updated May 14, 2019
  • dge_workflow: report number of reads per gene
    #51 · created May 31, 2019 by herseman
    • 14
    updated Jun 30, 2020
  • general: think about using argparser instead of docopt for futur scripts
    #52 · created Jun 03, 2019 by herseman
    • CLOSED
    • 6
    updated May 26, 2020
  • general: Test packrat for keep reproducible R environments
    #53 · created Jun 04, 2019 by domingue
    • CLOSED
    • 4
    updated Sep 16, 2019
  • general: add multiQC report to fastqc_summary
    #54 · created Jun 05, 2019 by herseman
    • CLOSED
    • 4
    updated Dec 02, 2019
  • dge_workflow: include MA plot from ggpubr in dge report
    #55 · created Jun 07, 2019 by herseman
    • CLOSED
    • 1
    updated Jun 18, 2019
  • 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
  • dge_workflow: error message because gtf_file did not exist
    #58 · created Jun 27, 2019 by herseman
    • CLOSED
    • 1
    updated Jun 27, 2019
  • MS worflow: improvements
    #59 · created Jul 17, 2019 by domingue
    • CLOSED
    • 10
    updated Aug 07, 2019
  • ms_workflow: add intensities to results table
    #60 · created Aug 09, 2019 by domingue   mass_spec
    • CLOSED
    • 2
    updated Aug 09, 2019
  • ms_workflow: add % of NAs to results table
    #61 · created Aug 09, 2019 by domingue   mass_spec
    • CLOSED
    • 1
    updated Aug 09, 2019
  • ms_workflow: replace PCA with plotly
    #62 · created Aug 09, 2019 by domingue   mass_spec
    • CLOSED
    • 2
    updated Aug 09, 2019
  • ms_workflow: add more explanations
    #63 · created Aug 09, 2019 by domingue   mass_spec
    • CLOSED
    • 1
    updated Aug 09, 2019
  • ms_workflow: QC improvments
    #64 · created Aug 09, 2019 by domingue   mass_spec
    • CLOSED
    • 1
    updated Aug 13, 2019
  • DEP installation on falcon - nc-config missing
    #65 · created Aug 14, 2019 by domingue   mass_spec
    • CLOSED
    • 1
    updated Sep 17, 2019
  • ms_workflow: improve the results heatmap   2 of 3 tasks completed
    #66 · created Aug 15, 2019 by domingue   mass_spec
    • 1
    updated Aug 23, 2019
  • expression_explorer: harcoded Rscipt path
    #67 · created Aug 15, 2019 by domingue   rna_seq
    • CLOSED
    • 0
    updated Aug 21, 2019
  • ms_workflow: Add table with % of contaminants in the most abudant proteins
    #68 · created Aug 26, 2019 by domingue   mass_spec
    • CLOSED
    • 0
    updated Aug 26, 2019
  • ms_worflow: bug in heatmap clustering
    #69 · created Aug 27, 2019 by domingue   mass_spec
    • CLOSED
    • 1
    updated Aug 28, 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
  • conda and bioconductor version
    #77 · created Jan 14, 2020 by domingue
    • CLOSED
    • 9
    updated Jan 21, 2020
  • Create stable conda enviroment for Single cell analysis conda on falcon
    #78 · created Jan 16, 2020 by domingue
    • CLOSED
    • 11
    updated Jul 08, 2020
  • updating ms_workflow
    #79 · created Jan 23, 2020 by herseman   mass_spec
    • CLOSED
    • 14
    updated Jul 13, 2020
  • MS: How is imputation done?
    #80 · created Jul 19, 2019 by domingue
    • CLOSED
    • 5
    updated Jan 24, 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
  • general: track unsynchronized files on the cluster
    #82 · created Feb 17, 2020 by herseman
    • CLOSED
    • 1
    updated Feb 17, 2020
  • ms_workflow: refine reorder information of protein groups
    #83 · created Feb 18, 2020 by herseman   mass_spec
    • CLOSED
    • 1
    updated Feb 18, 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
  • ms_workflow: ms_ms_prop and reorder information are missing for protein IDs without fasta_header information
    #86 · created Mar 17, 2020 by herseman   mass_spec
    • CLOSED
    • 1
    updated Mar 17, 2020
  • Move workflows to separate repositories
    #87 · created Mar 19, 2020 by domingue
    • CLOSED
    • 4
    updated Mar 20, 2020
  • Stranded counts
    #88 · created Mar 27, 2020 by domingue   rna_seq
    • 5
    updated Jul 13, 2020
  • general: create new human igenome for the Ensembl release 99
    #89 · created Jun 24, 2020 by herseman
    • CLOSED
    • 0
    updated Jun 24, 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
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