snakemake-workflows rna-seq-star-deseq2 issues

snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

MIT License

327 stars 203 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Bugfix

#41 kilpert closed 1 year ago
2
Bugfix

#40 kilpert closed 3 years ago
0
Gene2symbol

#39 jafors closed 3 years ago
0
fix formatting for new version of super-linter

#38 jafors closed 3 years ago
0
Adapting Lparsons updates

#37 jafors closed 3 years ago
0
Remove deprecated `config.yaml`

#36 vinisalazar closed 3 years ago
0
Changes to output normalized counts during deseq2-init

#35 jafors closed 3 years ago
0
snakedeploy fails to deploy workflow

#34 vkkodali closed 2 years ago
3
Reformatting and additions to meet workflow standards

#33 jafors closed 3 years ago
0
count-matrix.py

#32 sunhuaiyu closed 1 year ago
4
Update dependencies and wrapper to more recent versions

#31 lparsons closed 3 years ago
3
More user-friendly version with additional options and more contrast options

#30 Jukre111 closed 3 years ago
3
gffutils from conda-forge

#29 geparada closed 1 year ago
1
fix get_contrast

#28 geparada closed 1 year ago
1
DESeq2 Plots Incorrectly Displayed

#27 tjbencomo closed 1 year ago
7
snakemake version 5.9.1 raised an error with get_deseq2_threads called as a pointer

#26 ginolhac closed 1 year ago
1
rule rseqc_gtf2bed failing with test dataset

#25 ScientistSMC closed 1 year ago
2
Ubuntu 18.04.2 LTS - raise sp.CalledProcessError(retcode, cmd)

#24 EasyPiPi closed 5 years ago
4
Missing input files for rule rseqc_gtf2bed

#23 EasyPiPi closed 5 years ago
3
Trimming now optional

#22 sschmeier closed 5 years ago
1
More a discussion point: Should trimming be made optional

#21 sschmeier closed 5 years ago
2
support for interactions

#20 phspo closed 5 years ago
2
Add Awareness of protocol strandedness

#19 matrs closed 5 years ago
4
`count-matrix.py` isn't for stranded RNA-seq protocols

#18 matrs closed 5 years ago
2
annotation.bed file size zero

#17 jy-nam closed 1 year ago
4
rseqc version 3.0.0

#16 sschmeier closed 5 years ago
1
Prefered way to do several idependent runs

#15 sschmeier closed 5 years ago
10
QC

#14 sschmeier closed 5 years ago
3
Added qc ruleset. Do QC based on rseqc and multiqc.

#13 sschmeier closed 5 years ago
2
Do not pass pandas object to count script as divergent pandas version…

#12 johanneskoester closed 5 years ago
0
fq1 is not None (rule align)

#11 mgalland closed 1 year ago
8
deseq2-init.R returned non-zero exit status 1.

#10 sateeshperi closed 5 years ago
18
Rule count_matrix job submission fails when used with --cluster parameter

#9 ManavalanG closed 6 years ago
3
Report

#8 johanneskoester closed 6 years ago
0
Validate configuration data via JSON schemas.

#7 johanneskoester closed 6 years ago
1
Adjusting output based on multiple types of input (single end vs paired end)

#6 john-lee-johnson closed 6 years ago
2
How to add quality control step (fastq_screen) to pipeline

#5 john-lee-johnson closed 6 years ago
2
Confusion about the trimming for single-end data

#4 john-lee-johnson closed 6 years ago
2
deseq2 error in SummarizedExperiment and GenomicRanges

#3 DavyCats closed 6 years ago
2
Enable definition of sequencing units (technical replicates or lanes)

#2 johanneskoester closed 6 years ago
0
Automatically infer reasonable values for threading in deseq2 rules.

#1 johanneskoester closed 7 years ago
0