Issues · bioinfo / ngs_tools · GitLab

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
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
impl better means to access summary and quality statististcs

#18 · created May 30, 2017 by brandl
- CLOSED
- 0
updated Nov 09, 2017
Add pcr duplication analysis for rna-seq workflow

#6 · created Apr 22, 2016 by brandl rna_seq
- CLOSED
- 0
updated Nov 09, 2017
Add groupGo to cp_enrichment

#4 · created Mar 16, 2016 by brandl
- CLOSED
- 1
updated Nov 09, 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
write shiny app (results relative local app) for dge data

#22 · created Nov 09, 2017 by herseman
- CLOSED
- 0
updated Jan 19, 2018
new ticket

#27 · created Nov 15, 2018 by brandl 3h
- CLOSED
- 3
updated Dec 07, 2018
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 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
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
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: 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: 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
add frip statistic to cs-workflow

#5 · created Mar 18, 2016 by brandl
- CLOSED
- 1
updated Mar 07, 2019

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