Issues · bioinfo / ngs_tools

New issue

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