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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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Merge activeDev 4.0.6 into master
#483
slsevilla
closed
1 year ago
0
test
#482
pajailwala
closed
1 year ago
0
Move Pipeliner to Biowulf8
#481
slsevilla
closed
1 year ago
2
Cleanup of branches / versions / Biowulf
#480
slsevilla
closed
1 year ago
2
exome pipeline subjobs suspend
#479
faridrashidi
closed
1 year ago
2
groups.tab: Add validation test
#478
kopardev
opened
1 year ago
0
Fix mmul FASTQ screen; currently not using mmul as a species
#477
slsevilla
closed
1 year ago
6
RNASeq DE naming error due to "." in sample
#476
slsevilla
opened
1 year ago
1
Genome.json file error with pipeliner v4.0.2
#475
slsevilla
closed
1 year ago
3
Use msigdb for pathway analysis; perform additional analysis on specific db/pathway
#474
slsevilla
opened
1 year ago
1
PIM not working for custom genome
#473
ky66
closed
2 years ago
1
ChIP-seq pipeline improvements
#472
tovahmarkowitz
closed
1 year ago
0
Custom Reference Genome and GTF file
#471
ky66
closed
1 year ago
3
miRseq pipeline
#470
shaoli86
closed
2 years ago
4
ChildIOException: File/directory is a child to another output
#469
matthewangel
closed
2 years ago
3
(master branch) Run freec only for hg38 and hg19
#468
mtandon09
closed
2 years ago
0
Run freec only for hg38 and hg19
#467
mtandon09
closed
2 years ago
0
Fixing reference to /scratch in novocraft sort rule in activeDev
#466
mtandon09
closed
2 years ago
1
Fixing reference to /scratch in novocraft sort rule
#465
mtandon09
closed
2 years ago
1
Variant Calling for RNAseq (hg38) stopped at star_align_2
#464
tangwei1129
closed
3 years ago
15
scRNA QC and integration fixes
#463
wong-nw
closed
3 years ago
0
Parse GTF on the fly
#462
kopardev
opened
3 years ago
1
Move to STAR version >= 2.7.6a
#461
kopardev
opened
3 years ago
1
ChIP-seq improvements
#460
tovahmarkowitz
closed
3 years ago
1
Improvement to differential expression html reports
#459
tovahmarkowitz
opened
3 years ago
0
Calculate actual mean fragment length for PE data. Use for sicer PE.
#458
tovahmarkowitz
opened
3 years ago
0
Fix error with PE duplicate removal. Incorporate Vishal's code.
#457
tovahmarkowitz
opened
3 years ago
0
Trimming adapters
#456
ky66
closed
3 years ago
1
miRSeq DE
#455
wong-nw
opened
4 years ago
0
scrnaDE
#454
wong-nw
opened
4 years ago
0
scrnaQC_Reports.R: New Rmd for all SingleR annotations
#453
wong-nw
opened
4 years ago
0
scrnaQC.R: Adjust image title and axis-label size
#452
wong-nw
opened
4 years ago
0
Improved QC Reports - June 2020 (NW)
#451
wong-nw
closed
3 years ago
1
ChIP-seq updates: estimated fragment length and more
#450
tovahmarkowitz
closed
4 years ago
0
Bug Fix in integrateBatches.R URD call
#449
wong-nw
closed
4 years ago
0
Pulling in AVIA patch and latest the single-cell improvements
#448
skchronicles
closed
4 years ago
0
Fixes for exome-seq, RNA-fusion pipeliens
#447
mtandon09
closed
4 years ago
0
Active dev
#446
mtandon09
closed
4 years ago
0
Active dev
#445
mtandon09
closed
4 years ago
0
Merging activeDev for v4.0.1 release
#444
skchronicles
closed
4 years ago
1
Adjust code to allow for user to adjust estimated fragment length
#443
tovahmarkowitz
closed
4 years ago
0
Fix glitches with DiffBind analysis
#442
tovahmarkowitz
opened
4 years ago
0
Update README
#441
skchronicles
closed
2 years ago
0
Python 2.7 module should be explicitly specified in all Pipeliner Rules. Python 2.7 will not be the default on biowulf.
#440
kopardev
closed
4 years ago
2
Fix sequenza error
#439
mtandon09
closed
4 years ago
0
scRNASeq changes Feb 2020
#438
wong-nw
closed
4 years ago
0
Scrnaseq
#437
wong-nw
closed
4 years ago
0
Scrnaseq - NW
#436
wong-nw
closed
4 years ago
0
Scrnaseq
#435
wong-nw
closed
4 years ago
0
Mirseq
#434
wong-nw
closed
4 years ago
0
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