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BIMSBbioinfo
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pigx_rnaseq
Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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Cannot be built with Snakemake 5
#46
rekado
closed
5 years ago
1
Interactive plot and GO results are blank (R 3.5)
#45
Nicolai-vKuegelgen
closed
3 years ago
4
expose STAR's optional tool arguments to the user
#44
borauyar
closed
5 years ago
1
Rule all / 'final-report' doesn't include STAR counts
#43
Nicolai-vKuegelgen
closed
5 years ago
1
Integrate splicing analysis
#42
frenkiboy
opened
5 years ago
0
move tool specific default arguments from snakefile to settings.yaml
#41
borauyar
closed
5 years ago
1
integrate RUVseq for batch correction
#40
borauyar
opened
5 years ago
1
set g:profiler base url
#39
borauyar
opened
6 years ago
1
GO analysis report
#38
Nicolai-vKuegelgen
closed
6 years ago
1
Combined (DEseq) results
#37
Nicolai-vKuegelgen
closed
4 months ago
2
Diagnostic plots
#36
Nicolai-vKuegelgen
closed
6 years ago
2
Annotation of salmon based counts
#35
Nicolai-vKuegelgen
closed
2 years ago
5
STAR based counts are always strand-unspecific
#34
Nicolai-vKuegelgen
closed
5 years ago
1
Putting fastq files in a subfolder leads to filepath/name problems later on
#33
Nicolai-vKuegelgen
closed
2 years ago
3
DESeq result table headers
#32
Nicolai-vKuegelgen
closed
6 years ago
1
harmonize documentation
#31
borauyar
closed
6 years ago
2
etc/settings.yaml.in needs to include default for cdna-fasta
#30
rekado
closed
6 years ago
1
bam index should have suffix .bam.bai, not only .bai
#29
alexg9010
closed
6 years ago
1
add disease ontology analysis module
#28
borauyar
opened
6 years ago
1
html reports too large
#27
borauyar
closed
6 years ago
1
fastqc error on max-cluster
#26
alexg9010
closed
6 years ago
10
Add Genome Browser Tracks
#25
alexg9010
closed
5 years ago
7
add additional arguments to qsub; this addresses https://github.com/B…
#24
alexg9010
closed
6 years ago
1
allow spaces in sample names?
#23
jonathanronen
closed
2 years ago
3
Salmon quant crashed
#22
alexg9010
closed
6 years ago
4
Star Map crashed
#21
alexg9010
closed
6 years ago
5
Add workflow description to authorea document
#20
Blosberg
closed
6 years ago
1
replace bamCoverage with bedtools genomecov
#19
borauyar
closed
6 years ago
0
(maybe) missing default value for some cluster config
#18
jonathanronen
closed
6 years ago
0
Use of Salmon leads to non-deterministic reports
#17
rekado
opened
6 years ago
1
Print generated report files upon successful execution
#16
rekado
closed
6 years ago
0
Include version in report
#15
rekado
closed
6 years ago
0
Documentation: make the README and Final report clear.
#14
Blosberg
closed
6 years ago
1
Validate sample sheet
#13
Blosberg
closed
6 years ago
0
make distcheck fails
#12
Blosberg
closed
6 years ago
1
logo missing
#11
alexg9010
closed
6 years ago
0
Make reports deterministic
#10
rekado
closed
6 years ago
1
Add license.
#9
rekado
closed
6 years ago
0
Set PYTHONPATH and R_LIBS_SITE.
#8
rekado
closed
6 years ago
1
update installation and execution instructions
#7
rekado
closed
6 years ago
0
ignore case in sample sheet header
#6
rekado
opened
6 years ago
2
optionally resolve input and output locations relative to cwd
#5
rekado
closed
6 years ago
0
add simple test script
#4
rekado
closed
6 years ago
0
add autotools support
#3
rekado
closed
6 years ago
0
support cluster submission
#2
rekado
closed
6 years ago
0
write launcher script
#1
rekado
closed
6 years ago
0
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