Issues · bioinfo / ngs_tools

New issue

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
run kallisto parallel to STAR

#21 · created Nov 09, 2017 by herseman
- 0
updated Nov 09, 2017
report proportion of multi-mappers in STAR report

#20 · created Nov 09, 2017 by herseman
- 0
updated Nov 16, 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
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
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
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