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SystemsGenetics
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GEMmaker
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
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Automatic cleanup with nf-boost
#289
bentsherman
opened
2 months ago
0
fastq_merge is very inefficent
#288
JohnHadish
opened
3 months ago
1
Stringtie prepDE.py script does not take sequence length into consideration
#287
JohnHadish
opened
5 months ago
1
Update README.md
#286
JohnHadish
closed
5 months ago
3
MultiQC for STAR alignment incorrect
#285
Huiting120
opened
5 months ago
1
withLabel does not work
#284
Huiting120
opened
8 months ago
0
GEMmaker not pulling test files (failed to pull sample URLs)
#283
feltus
opened
8 months ago
0
nextflow cannot open cache dir
#282
abbye1093
opened
10 months ago
1
GEMmaker not running
#281
ldunwoodie
opened
10 months ago
2
Running local files through trimmomatic fails if file does not end with ".fastq" (e.g. ."fq")
#280
JohnHadish
opened
10 months ago
2
Log File Should Occasionally output system time
#279
JohnHadish
opened
1 year ago
0
GEMmaker documentation--using gffread to make GTF file
#278
ko0000
opened
1 year ago
0
GEMMAKER not writing results after very quick run time on Clemson Palmetto cluster
#277
feltus
opened
1 year ago
2
GEMMAKER broken at metadata retrieval again
#276
feltus
closed
1 year ago
1
Dev
#275
spficklin
closed
1 year ago
2
Where to change path:prefix so GEMMAKER runs?
#274
feltus
closed
1 year ago
2
create_gem rewrite with `join`
#273
JohnHadish
opened
1 year ago
0
Deleted Code which is never referenced
#272
JohnHadish
closed
1 year ago
3
`baseDir` has been deprecated
#271
JohnHadish
opened
1 year ago
0
Not able to modify fastq_merge memory default
#270
JohnHadish
opened
1 year ago
3
Log file cuts at 80 characters
#269
JohnHadish
opened
1 year ago
0
Fail on resume due to file not being present in stage directory
#268
JohnHadish
opened
1 year ago
1
GEMmaker no longer creates nextflow reports by default
#267
JohnHadish
opened
1 year ago
3
StringTie prepDE.py script needs length argument for calculating raw counts
#266
JohnHadish
opened
1 year ago
1
Output GEM format is not tidy
#265
JohnHadish
opened
1 year ago
0
Documentation Fixes
#264
spficklin
opened
1 year ago
0
clean_work_dirs bug
#263
cbmckni
opened
2 years ago
3
Need to Increase Number of lines in output
#262
JohnHadish
opened
2 years ago
0
Report of Default Memory, time, etc.
#261
JohnHadish
opened
2 years ago
0
Updates to docs
#260
spficklin
opened
2 years ago
0
Edge Case Fastq Merge
#259
JohnHadish
opened
2 years ago
2
Publish metadata
#258
spficklin
opened
2 years ago
0
New release PR
#257
spficklin
closed
2 years ago
3
Samtool "% Mapped" is unneccesary
#256
JohnHadish
opened
2 years ago
0
Hisat2 unmapped read optional cleanup
#255
JohnHadish
opened
2 years ago
0
Star
#254
JohnHadish
closed
2 years ago
2
Star
#253
JohnHadish
closed
2 years ago
3
dev branch: Kallisto only Workflow that can process paired files
#252
JohnHadish
closed
2 years ago
2
Fix for GEM creation
#251
spficklin
closed
2 years ago
0
FPKM, TPM and raw GEMs have different column orders for samples
#250
JohnHadish
opened
2 years ago
0
nf-core DSL2 compatibilty
#249
spficklin
closed
2 years ago
6
GEMmaker is "failing" according to front page of github
#248
JohnHadish
closed
2 years ago
3
Add a cleanup script for failed work directories
#247
spficklin
opened
2 years ago
0
Replace baseDir with projectDir
#246
bentsherman
closed
2 years ago
2
Upgrade to DSL 2 syntax
#245
bentsherman
closed
2 years ago
8
Permission denied
#244
spficklin
opened
2 years ago
0
added info for Issue 236
#243
JohnHadish
closed
2 years ago
0
Added fix for Issue 233
#242
JohnHadish
closed
2 years ago
1
Palmetto-related tweaks
#241
bentsherman
closed
2 years ago
3
Palmetto fixes
#240
bentsherman
closed
2 years ago
2
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