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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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`record_annotation_files` uses uncaptured tools
#145
rekado
opened
3 weeks ago
1
Tibanna
#144
rekado
closed
1 month ago
0
Fix for issue#140
#143
FrancescoSantini
closed
2 months ago
1
Changing the cDNA fasta should not trigger rerun of hisat2 branch
#142
alexg9010
opened
2 months ago
0
Local build of pipeline fails to run on cluster
#141
alexg9010
opened
2 months ago
2
Pipeline fails on settings file without DEA when trying to collate deseq reports
#140
alexg9010
closed
2 months ago
3
Issues/138
#139
alexg9010
closed
2 months ago
1
Fix mismatching names for cluster config and Snakefile
#138
alexg9010
closed
2 months ago
6
Pandoc error when running using cluster submission
#137
alexg9010
opened
2 months ago
6
Added short script to collate deseq_results.tsv from all the differen…
#136
FrancescoSantini
closed
4 months ago
0
Collating Salmon counts fails
#135
borauyar
closed
7 months ago
0
Copy/link the annotation in the results folder
#134
frenkiboy
closed
7 months ago
0
Error when submitting to cluster
#133
Pinolinoo
closed
7 months ago
21
error when executing
#132
Pinolinoo
closed
1 year ago
3
yieldSize hardcoded in count_reads.R
#131
kerimsecener
closed
7 months ago
0
salmon results show no gene names - with latest guix rnaseq 0.1
#130
smoe
opened
1 year ago
6
add a module for gene-set enrichment analysis
#129
borauyar
opened
2 years ago
0
Rule specific memory requirements are not respected in cluster submission
#128
borauyar
closed
2 months ago
12
suggesting singularity image
#127
smoe
closed
2 years ago
3
suggesting runtime tests
#126
smoe
opened
2 years ago
4
Outdated m4/ax_r_package.m4
#125
tillea
closed
2 years ago
1
scripts/collate: header is always needed, not 'auto'
#124
smoe
closed
2 years ago
1
samtools: files already existing
#123
smoe
closed
2 years ago
3
suggesting check of covariates against sample sheet column names
#122
smoe
closed
2 years ago
0
Passing 'selfContained' as parameter
#121
smoe
closed
2 years ago
3
Passing description from settings.yaml to report.
#120
smoe
closed
2 years ago
2
gprofiler2 report not shown with DT::datatable
#119
smoe
closed
2 years ago
8
Helping local execution of code producing figures
#118
smoe
closed
2 years ago
2
sample_sheets - accept experiments without a fastq file referenced
#117
smoe
closed
2 years ago
3
idea how to print instruction to directly set paths to reproduce analysis
#116
smoe
closed
2 years ago
2
Code shown in Report does not define "params"
#115
smoe
closed
2 years ago
2
Paired analyses?
#114
smoe
closed
2 years ago
2
Avoid runtime error during merge, no headers in table
#113
smoe
closed
2 years ago
6
default settings.yaml lacks 'log-dir' specification
#112
smoe
closed
2 years ago
3
Spreadsheet-generated sample_sheet not properly importable - early warning?
#111
smoe
closed
2 years ago
7
Slurm as a queuing system for pigx-rnaseq? Or generally abstract away from gridengine?
#110
smoe
closed
2 years ago
2
Warn about genome reference data remaining compressed
#109
smoe
closed
2 years ago
1
Detecting blanks in flanks of samples' filenames
#108
smoe
closed
2 years ago
1
hisat2-build expects fasta file, doe not accept fasta.gz - maybe warn earlier?
#107
smoe
closed
2 years ago
2
Check for blanks in filename when samples are not found
#106
smoe
closed
2 years ago
4
Multiple fastq input files per sample?
#105
smoe
closed
2 years ago
3
'pandoc-citeproc' not in requirements
#104
robert-altwasser
closed
2 years ago
1
all rules should have `resources`
#103
rekado
closed
2 years ago
4
add megadepth for fast genome coverage computation
#102
borauyar
closed
2 years ago
2
update settings template to include log-dir option
#101
borauyar
closed
2 years ago
0
Allow pre-built genome indices as input
#100
borauyar
opened
2 years ago
0
Analysis name in "DEanalyses" section must be quoted
#99
rekado
opened
2 years ago
1
CI tests with Debian?
#98
smoe
opened
3 years ago
2
add snakemake resources + memory requirements per rule
#97
rekado
closed
3 years ago
1
MissingOutputException for "samtools index" with 0.0.13
#96
smoe
closed
3 years ago
2
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