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CCBR
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Pipeliner
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
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Mirseq_NW_20191112
#433
wong-nw
closed
4 years ago
1
Specify R version
#432
mtandon09
closed
4 years ago
0
fixed gzipped VCF bug in exam and WGS pipelines
#431
jlac
closed
4 years ago
0
update hg38 PON
#430
jlac
closed
4 years ago
0
Bam2bw fix with changes
#429
kopardev
closed
4 years ago
1
added missing tail -n1 bam2bw rule
#428
kopardev
closed
4 years ago
0
D1.0 type fixed to 1.0 in bam2bw rule
#427
kopardev
closed
4 years ago
0
Added merged output for FusionInspector and Oncofuse across STARfusion and FusionCatcher
#426
jlac
closed
4 years ago
0
bam2bw fix
#425
kopardev
closed
4 years ago
0
Active dev
#424
kopardev
closed
4 years ago
0
ChIP-seq: differential peak calling and more
#423
tovahmarkowitz
closed
4 years ago
0
switch VarDict to java version for faster run time
#422
jlac
closed
5 years ago
0
reduced verbosity of VarDict and added MutSigCV for additional callers
#421
jlac
closed
5 years ago
0
Added multi-variant calling to all somatic variant detection Pipelines
#420
jlac
closed
5 years ago
0
RNA-seq, rule rseqc, infer_experiment.py and read_distribution.py are missing
#419
acgtcoder
closed
5 years ago
5
miRSeq pipeline
#418
wong-nw
closed
4 years ago
1
ChIP-seq multiQC improvements, and a few other minor details
#417
tovahmarkowitz
closed
5 years ago
1
improve handling of cluster.json for troubleshooting
#416
tovahmarkowitz
closed
5 years ago
0
RNA-seq: Adding Support for canFam3 (Canis lupus familiaris) and Mmul_8.0.1 (Macaca mulatta)
#415
skchronicles
closed
5 years ago
0
Expand Kraken databases
#414
kopardev
closed
4 years ago
0
adjust sicer conditions in chip-sea pipeline
#413
tovahmarkowitz
closed
5 years ago
0
add dfilter to ChIP-seq pipeline
#412
tovahmarkowitz
closed
4 years ago
2
ChIPQC
#411
tovahmarkowitz
opened
5 years ago
0
improve IDR
#410
tovahmarkowitz
opened
5 years ago
0
Delta-delta in contrasts.tab
#409
wong-nw
opened
5 years ago
1
New and improved ChIP-seq peak calling and associated tools.
#408
tovahmarkowitz
closed
5 years ago
1
contrasts.tab
#407
kopardev
closed
5 years ago
1
fixed bug in prep_mafs.pl script
#406
jlac
closed
5 years ago
0
Preseq lc_extrap: Too many defects in the approximation
#405
skchronicles
closed
5 years ago
0
improved somatic variant filtering and maftools summaries
#404
jlac
closed
5 years ago
0
PhantomPeakQualTool: Estimated Fragment Length
#403
skchronicles
closed
5 years ago
0
RNA-seq problem: Error in rule trim_pe:
#402
yuguoyun
closed
5 years ago
2
fixed bug in WES BED file generation
#401
jlac
closed
5 years ago
0
moved sort out of STAR and into samtools rule to deal with memory bug
#400
jlac
closed
5 years ago
0
PCA Report: Before Normalization and DESeq2
#399
skchronicles
closed
5 years ago
1
set memory limit for STAR 2-pass BAM sort
#398
jlac
closed
5 years ago
0
fixed bug tracking FREEC 2nd pass output
#397
jlac
closed
5 years ago
0
Added FREEC and Sequenza CNV calling
#396
jlac
closed
5 years ago
0
bam2bw uses actual genome size not effective genome size
#395
tovahmarkowitz
closed
4 years ago
0
adding ngsqc plot feature
#394
tovahmarkowitz
closed
5 years ago
0
fix QC issues with dedups
#393
tovahmarkowitz
closed
5 years ago
0
Add peak call options on GUI
#392
tovahmarkowitz
closed
4 years ago
1
adding macs2 dedup functionality
#391
tovahmarkowitz
closed
5 years ago
0
Excel-friendly DEG Result
#390
skchronicles
opened
5 years ago
1
moved somatic filtering out of maftools and updated somatic gVCF genotyping to GATK3.8
#389
jlac
closed
5 years ago
0
fixed fingerprint plot and multiQC
#388
tovahmarkowitz
closed
5 years ago
0
Bigwigs for RNASeq
#387
kopardev
closed
4 years ago
0
fingerprint plot and multiQC
#386
tovahmarkowitz
closed
5 years ago
0
Adding Calendar and Seminar Information [ABCSfrederick]
#385
skchronicles
closed
5 years ago
0
fix bam headers
#384
tovahmarkowitz
opened
5 years ago
0
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