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bioinfo
ngs_tools
Issues
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3
Closed
34
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37
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Manual
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Last updated
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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
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
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
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
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
expression_explorer: harcoded Rscipt path
#67
· created
Aug 15, 2019
by
domingue
rna_seq
CLOSED
0
updated
Aug 21, 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
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
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
Stranded counts
#88
· created
Mar 27, 2020
by
domingue
rna_seq
5
updated
Jul 13, 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
GSEA: improve color code of KEGG pathways
#101
· created
Mar 23, 2021
by
gohr
rna_seq
CLOSED
0
updated
Mar 23, 2021
gsea: improvement of description
#102
· created
Apr 08, 2021
by
gohr
Bioinformatics
Internal
Non-rechargeable
rna_seq
CLOSED
1
updated
Apr 08, 2021
gsea: fixing expression explorer
#103
· created
Apr 08, 2021
by
gohr
Bioinformatics
Internal
Non-rechargeable
rna_seq
CLOSED
0
updated
Apr 08, 2021