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bioinfo
ngs_tools
Issues
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15
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88
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103
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Title
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
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