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CCBR
/
RENEE
A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
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ResourceWarning in v2.6
#160
kelly-sovacool
opened
5 days ago
0
add debug subcommand
#159
kelly-sovacool
closed
1 week ago
0
chore: 🤖 prepare release v2.6.0
#158
github-actions[bot]
closed
2 weeks ago
0
chore: specify ccbr_tools version v0.1.0
#157
kelly-sovacool
closed
1 month ago
0
Update doc website with more FAQs and expect output tab
#156
samarth8392
closed
1 month ago
2
error running jobby
#155
kelly-sovacool
closed
1 month ago
3
fix: always load required modules
#154
kelly-sovacool
closed
1 month ago
0
bug: snakemake issue in shared conda env on biowulf
#153
kelly-sovacool
closed
1 month ago
1
fix: switch image paths in README to perma URLs
#152
kelly-sovacool
closed
1 month ago
0
Use tools package
#151
kelly-sovacool
closed
1 month ago
1
docs: use mike for multiple docs versions on website
#150
kelly-sovacool
closed
1 month ago
0
feat: rsem-generate-data-matrix for genes & isoforms
#149
kelly-sovacool
closed
1 month ago
0
improve slurm complete/error email to describe where the pipeline output is
#148
kelly-sovacool
opened
1 month ago
0
docs: FAQ on searching for failed jobs in log files
#147
kelly-sovacool
closed
1 month ago
2
docs: describe outputs
#146
kelly-sovacool
closed
1 month ago
0
deprecate older genome versions after ~1 year, link to dockstore
#145
kelly-sovacool
opened
1 month ago
0
feature: DTU - differential transcript usage
#144
kelly-sovacool
opened
1 month ago
0
ci: pytest module import
#143
kelly-sovacool
closed
1 month ago
0
ci: fix job names
#142
kelly-sovacool
closed
1 month ago
0
doc: create documentation for GUI
#141
samarth8392
closed
1 month ago
1
write output fastq validator to a log file instead of an output file
#140
kelly-sovacool
opened
1 month ago
0
fix copy in safe mode
#139
kelly-sovacool
closed
1 month ago
0
change fasta for hg19
#138
kelly-sovacool
closed
1 month ago
1
Feature request: RSEM outputs - counts matrix for isoforms
#137
TBrownmiller
closed
1 month ago
5
Re-build human genome annotations with GDC fasta
#136
kelly-sovacool
closed
1 month ago
2
docs: link README to table of reference genomes
#135
kelly-sovacool
closed
3 months ago
0
Update docs (especially README) with list of supported genome versions
#134
kelly-sovacool
closed
3 months ago
0
docs: suggest --sif-cache in readme
#133
kelly-sovacool
closed
3 months ago
0
add --sif-cache flag to readme docs
#132
kelly-sovacool
closed
3 months ago
0
fix: show renee <subcommand> for help messages rather than python script
#131
kelly-sovacool
closed
4 months ago
0
`--help` functions report the name of the pipeline to be `__main__.py`
#130
kopardev
closed
1 month ago
2
Change human reference fasta
#129
kopardev
closed
1 month ago
3
set default human genome+annotation combo to match GDC
#128
kopardev
closed
1 month ago
3
feat: add hg38 v45 reference genome
#127
kelly-sovacool
closed
4 months ago
3
add support for v45 reference from gencode
#126
kopardev
closed
4 months ago
3
consolidate build_cluster.json with cluster.json
#125
kelly-sovacool
opened
5 months ago
0
chore: prepare release v2.5.12
#124
github-actions[bot]
closed
5 months ago
0
fix: update rseqc docker
#123
kelly-sovacool
closed
5 months ago
1
fix: update rseqc module to v4.0.0
#122
kelly-sovacool
closed
5 months ago
0
snakemake/singularity loading error on main branch of 2.5.11-dev
#121
slsevilla
closed
5 months ago
3
RSEQC version on biowulf has been updated
#120
slsevilla
closed
5 months ago
8
Error called in RSEM, TIN, BAM2BW: python 3.12 missing from user path
#119
slsevilla
closed
5 months ago
17
Add QC check if no reads are left after `cutadapt`
#118
slsevilla
opened
7 months ago
1
RNA Report is failing with too few samples.
#117
slsevilla
opened
7 months ago
0
STAR command is not using TMP dir - moving and removing files created in the outputdir
#116
slsevilla
opened
7 months ago
0
test: show that sif images are cached correctly
#115
kelly-sovacool
closed
7 months ago
0
test: setup basic cli tests with pytest
#114
kelly-sovacool
closed
7 months ago
4
SIF images not being copied from shared cache dir
#113
kelly-sovacool
closed
7 months ago
3
Feature request: Add "annoFuse"
#112
kopardev
opened
7 months ago
1
Feature Request: Add "STAR-Fusion"
#111
kopardev
opened
7 months ago
0
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