mskilab-org fragCounter issues

mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing

MIT License

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issues

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gc/mappability files tarred and readme updated

#30 jrafailov opened 6 months ago
1
updated hg19/hg38 GC/mappability files added

#29 jrafailov closed 6 months ago
0
GC and mappability corrected read depth data for hg38

#28 Bio-LiHe opened 7 months ago
1
Fix: Added a fix in CLI and fragCounter.R to take reference when cram files are used.

#27 tanubrata closed 8 months ago
1
update frag executable and add codecov.yml

#26 zining01 closed 1 year ago
0
Dev

#25 zining01 closed 1 year ago
0
calculate ratio between tumor and normal sample’s WGS read counts

#24 Bio-LiHe opened 1 year ago
1
Keep "chr" notation

#23 l0ka closed 1 year ago
6
Getting error 'Killed' upon running in docker container

#22 shashkat opened 1 year ago
0
migrate to gha

#21 zining01 closed 1 year ago
0
Error in the final step (R): 'by' appears to evaluate to column names but isn't c() or key()'

#20 Giuseppe1995 opened 2 years ago
1
invalid class "BigWigFile" error when running frag with bundled example files

#19 hillan141 opened 2 years ago
0
Expose cov

#18 ShaiberAlon opened 2 years ago
1
exposes --cov param

#17 zlskidmore opened 2 years ago
3
data.table breaks fragCounter

#16 jamesdalg opened 2 years ago
2
GC and mappability RDS files for hg19 WGS missing?

#15 ehjChun opened 2 years ago
0
unable to call "samtools"

#14 ehjChun opened 2 years ago
2
run test data and get an DNACopy error

#13 dagezh closed 1 year ago
4
Allow users to provide coverage data and only perform GC and mappability correction

#12 ShaiberAlon opened 2 years ago
0
CRAM support

#11 ppararaj closed 2 years ago
7
fragCounter: error from readChar(): line 924 in fragCounter.R

#10 chris-kreitzer closed 2 years ago
1
Added GC and mapability scores for hg38 200bp

#9 ShaiberAlon closed 3 years ago
0
FragCounter not reading from cov.rds files

#8 oriolpich opened 3 years ago
0
Error in multicoco

#7 alhafidzhamdan closed 3 years ago
12
build my own gc and map rds file

#6 jinghu23 opened 3 years ago
3
Correcting coverage for both hg19 and GRCh37

#5 kcygan opened 4 years ago
0
GC + mappability corrections

#4 tlesluyes opened 4 years ago
2
multicoco going wrong

#3 tlesluyes opened 4 years ago
1
minmapq is ignored

#2 tlesluyes opened 4 years ago
1
Do you have hg38 versions of the mappability and gc rds files?

#1 pwaltman closed 3 years ago
4