Issues · bioinfo / ngs_tools

New issue

auto-detect strandedness when extracting count matrix

#16 · created May 29, 2017 by brandl
- CLOSED
- 2
updated Mar 27, 2020
Move workflows to separate repositories

#87 · created Mar 19, 2020 by domingue
- CLOSED
- 4
updated Mar 20, 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
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
finish panther enrichment and reintegrate into cp_enrichment.R

#7 · created May 12, 2016 by brandl rna_seq
- CLOSED
- 2
updated Feb 20, 2020
iGenome permissions

#76 · created Nov 15, 2019 by domingue rna_seq
- CLOSED
- 0
updated Feb 20, 2020
Implement renvs

#73 · created Sep 16, 2019 by domingue mass_spec rna_seq
- CLOSED
- 2
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
report improvements

#25 · created Nov 16, 2017 by brandl
- CLOSED
- 1
updated Feb 20, 2020
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
ms_workflow: refine reorder information of protein groups

#83 · created Feb 18, 2020 by herseman mass_spec
- CLOSED
- 1
updated Feb 18, 2020
general: track unsynchronized files on the cluster

#82 · created Feb 17, 2020 by herseman
- CLOSED
- 1
updated Feb 17, 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
MS: How is imputation done?

#80 · created Jul 19, 2019 by domingue
- CLOSED
- 5
updated Jan 24, 2020
conda and bioconductor version

#77 · created Jan 14, 2020 by domingue
- CLOSED
- 9
updated Jan 21, 2020
ms_workflow: Improvemnts 7 of 9 tasks completed

#28 · created Dec 07, 2018 by brandl mass_spec
- CLOSED
- 3
updated Dec 10, 2019
ms_workflow: handling of contaminations

#37 · created Feb 08, 2019 by herseman mass_spec
- CLOSED
- 1
updated Dec 10, 2019
try RNA-SeQC to get qc for bam files

#15 · created May 19, 2017 by brandl
- CLOSED
- 1
updated Dec 09, 2019
general: add multiQC report to fastqc_summary

#54 · created Jun 05, 2019 by herseman
- CLOSED
- 4
updated Dec 02, 2019
dge_workflow: fix lcf help

#74 · created Oct 22, 2019 by domingue rna_seq
- CLOSED
- 0
updated Dec 02, 2019