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CCBR
/
CARLISLE
Cut And Run Analysis Pipeline
https://ccbr.github.io/CARLISLE/
MIT License
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chore: 🤖 prepare release v2.6.1
#150
github-actions[bot]
closed
1 month ago
0
fix: less specific module versions
#149
kelly-sovacool
closed
1 month ago
0
Python import error in carlisle v2.6.0
#148
kelly-sovacool
closed
1 month ago
0
chore: 🤖 prepare release v2.6.0
#147
github-actions[bot]
closed
2 months ago
0
set up mkdocs mike & release actions
#146
kelly-sovacool
closed
2 months ago
0
refactor: use bin/redirect from xavier
#145
kelly-sovacool
closed
2 months ago
0
refactor: use jobby & spooker from CCBR/Tools
#144
kelly-sovacool
closed
2 months ago
0
fix: new --singcache argument & set default singularity cache dir
#143
kelly-sovacool
closed
2 months ago
1
multiple versions for docs site
#142
kelly-sovacool
closed
2 months ago
0
rewrite CLI in python
#141
kelly-sovacool
opened
4 months ago
0
style: run prettier on all files
#140
kelly-sovacool
closed
2 months ago
0
fix: remove singularity version number
#139
kelly-sovacool
closed
4 months ago
0
singularity v3.10.5 will no longer be available on biowulf soon
#138
kelly-sovacool
closed
4 months ago
0
set singularity cachedir to WORKDIR/.singularity by default
#137
kelly-sovacool
closed
2 months ago
1
Add @epehrsson to authors
#136
kelly-sovacool
closed
6 months ago
1
fix singularity bind paths
#135
kelly-sovacool
closed
6 months ago
0
`rose` takes too long
#134
kelly-sovacool
opened
6 months ago
0
feat: add parameter to make long-running rules optional
#133
kelly-sovacool
closed
6 months ago
0
Add new rules visualizing CARLISLE results
#132
epehrsson
closed
5 months ago
4
`go_enrichment` rule takes >48 hours on test dataset
#131
kelly-sovacool
opened
7 months ago
1
refactor: simplify create_contrast_peakcaller_files
#130
kelly-sovacool
closed
7 months ago
0
Use docker container for rules that use R
#129
kelly-sovacool
closed
6 months ago
1
Switch to containers and remove code related to R library paths & R package installation
#128
kelly-sovacool
closed
6 months ago
0
Fixed bugs related to library normalization with no_dedup, replicate formatting, and DESeq
#127
epehrsson
closed
7 months ago
5
deseq2 sample check is failingi
#126
slsevilla
closed
7 months ago
1
GO enrichment is lagging with 'gopeaks' peak caller, during `linking distal enhancers`
#125
slsevilla
closed
9 months ago
0
rule findMotif fails for mm10
#124
epehrsson
opened
9 months ago
0
Error in rule bam2bg when running "no_dedup" option
#123
epehrsson
closed
7 months ago
1
Add rule go_enrichment for mm10
#122
epehrsson
opened
9 months ago
1
Pipeline does not launch for mm10 due to missing parameters
#121
epehrsson
closed
9 months ago
2
Update deeptools_mat to be genome-specific
#120
epehrsson
opened
9 months ago
0
Dryrun fails due to replicate formatting in samples.tsv
#119
epehrsson
closed
7 months ago
0
RLibs Path for all RMD files
#118
slsevilla
closed
9 months ago
1
Improve runtest defaults, add changelog, update --version flag, add --force flag, refactor Rlibs
#117
slsevilla
closed
9 months ago
4
add CHANGELOG
#116
slsevilla
closed
9 months ago
0
Improve runmode `testrun` by updating params, adding mm10
#115
slsevilla
closed
9 months ago
1
v2.4.1 changes from main
#114
slsevilla
closed
9 months ago
0
rumode testrun produces error with DESEQ2
#113
slsevilla
closed
9 months ago
3
`carlisle --version` should print version number
#112
kopardev
closed
9 months ago
0
Citation updates
#111
kelly-sovacool
closed
10 months ago
0
version 2.4.1 updates
#110
slsevilla
closed
10 months ago
0
DESEQ2 error when only 1 sample/group - test sample issue
#109
slsevilla
closed
10 months ago
0
feat: use summits bed for homer input; save temporary files; fix deseq2 bug
#108
slsevilla
closed
10 months ago
0
docs: adding citation and DOI to pipeline
#107
slsevilla
closed
10 months ago
0
Add citation and DOI
#106
slsevilla
closed
10 months ago
0
use summit.bed file as input for homer
#105
slsevilla
closed
10 months ago
1
save additional output files from pipeline
#104
slsevilla
closed
10 months ago
1
master yue requests from 12/7 (motif, save files)
#103
slsevilla
closed
10 months ago
1
allow for execution without a control
#102
slsevilla
opened
1 year ago
1
update spooker commands
#101
slsevilla
closed
10 months ago
1
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