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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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MissingOutputException for "samtools index" with 0.0.13
#96
smoe
closed
3 years ago
2
RNA-Seq pipeline stopping after trim galore
#95
kerimsecener
closed
3 years ago
1
Add hisat support
#94
rekado
closed
3 years ago
0
STAR -> Hisat2
#93
rekado
closed
3 years ago
1
Handle covariates setting in case it is missing - #82
#92
dohmjan
closed
3 years ago
0
replace export.bw with a better candidate
#91
frenkiboy
closed
3 years ago
2
Implement a secondary mapper with lower memory footprint
#90
frenkiboy
closed
3 years ago
4
Replace trimgalore with bbtrim
#89
frenkiboy
closed
3 years ago
2
It's the memory, stupid! How to solve the "cannot change locale" problem.
#88
smoe
closed
3 years ago
7
STAR - unknown parameter genomeType - after guix install pigx-rnaseq
#87
smoe
closed
3 years ago
5
'group_by' applied to an object of class "c('plotly', 'htmlwidget') - anyone?
#86
smoe
closed
2 years ago
9
Clarifying covariates setting
#85
smoe
closed
3 years ago
1
helping the user to find STAR setting
#84
smoe
closed
3 years ago
0
Allow configuration of STAR parameter --limitGenomeGenerateRAM
#83
smoe
closed
3 years ago
3
DEanalysis covariates should not be manadatory
#82
smoe
closed
3 years ago
5
counts from salmon / tximport crash when adding new samples to project
#81
Nicolai-vKuegelgen
closed
2 years ago
6
remove leading and trailing whitespaces from given target list
#80
alexg9010
opened
3 years ago
2
salmon does not produce sa.bin files -> pos.bin
#79
smoe
closed
3 years ago
2
test.sh on trimmed_reads misses file after successful execution
#78
smoe
closed
3 years ago
1
Use Drimseq for differential transcript analysis
#77
alexg9010
opened
3 years ago
0
counts from salmon fails for single sample
#76
alexg9010
opened
3 years ago
1
counts from salmon fails if sample_type is empty
#75
alexg9010
closed
2 years ago
1
crash when sample sheet contains empty lines
#74
rekado
closed
2 years ago
1
Allow multiple fastq file name endings (fastq, fq) - #71
#73
dohmjan
closed
4 years ago
0
upgrade gprofiler to gprofiler2
#72
borauyar
closed
3 years ago
0
File names ending in .fq.gz crash trim_galore rule
#71
Nicolai-vKuegelgen
closed
4 years ago
0
catching missing qsub error
#70
alexg9010
opened
4 years ago
0
stranded paired end data lead to unstranded bigWig files
#69
constadakis
closed
3 years ago
1
Adding cmd-line options for salmon via yaml doesn't work
#68
Nicolai-vKuegelgen
closed
3 years ago
1
tests: unknown fitType in DESeqDataSet - estimateDispersions
#67
smoe
closed
4 years ago
1
remove files from distribution that are created/changed/cleaned during/after build
#66
smoe
closed
3 years ago
4
make salmon count optional
#65
frenkiboy
closed
3 years ago
1
Re-rerunning multiQC causes a MissingOutputException
#64
Nicolai-vKuegelgen
closed
3 years ago
0
norm_counts_deseq fails if samplesheet is edited
#63
Nicolai-vKuegelgen
closed
2 years ago
1
Setting-option: count_nonunique
#62
Nicolai-vKuegelgen
closed
3 years ago
0
define resources for count_reads rule
#61
alexg9010
closed
3 years ago
0
(dist)clean cleans files in release and/or git
#60
smoe
closed
3 years ago
1
tximport not listed as requirement
#59
smoe
closed
4 years ago
1
reporting script fails when more than 8 sample type provided
#58
borauyar
closed
4 years ago
0
apply fastqc on fastq files before/after trimming
#57
borauyar
closed
3 years ago
1
improve validation script to try to fail early with meaningful messages
#56
borauyar
closed
2 years ago
2
split STAR index and STAR map arguments and expose arguments in settings
#55
borauyar
closed
4 years ago
0
export bigwig files rather than bedgraph files
#54
borauyar
closed
5 years ago
2
Missing conda environment.yml file
#53
fhorvat
closed
5 years ago
2
saving pheatmap to pdf produces corrupted file
#52
alexg9010
closed
5 years ago
0
STAR error when sorting bam files
#51
frenkiboy
closed
4 years ago
0
Output nice errors when settings files are not defined
#50
frenkiboy
closed
7 months ago
2
multiqc dies with large number of samples
#49
frenkiboy
opened
5 years ago
5
Pipeline does not work with unzipped input files
#48
frenkiboy
closed
3 years ago
1
Allow building with Snakemake 5.
#47
rekado
closed
5 years ago
0
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