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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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Documentation
#383
tovahmarkowitz
opened
5 years ago
0
peak annotations
#382
tovahmarkowitz
closed
5 years ago
0
handle replicates
#381
tovahmarkowitz
closed
4 years ago
0
clean up chipseq.snakefile
#380
tovahmarkowitz
closed
5 years ago
0
fix macs2 peak calling
#379
tovahmarkowitz
closed
5 years ago
0
improve fingerprint plot
#378
tovahmarkowitz
closed
5 years ago
0
GUI Warning Message: Whole Exome/Genome Pipelines
#377
skchronicles
closed
5 years ago
1
ChIP-seq changes
#376
tovahmarkowitz
closed
5 years ago
0
Generate reference FAI files for MEMEchip
#375
skchronicles
closed
5 years ago
2
Python Package Import Incompatibility: pysam
#374
skchronicles
closed
5 years ago
3
fixed SnpEff bug in variant annotation
#373
jlac
closed
5 years ago
0
Fix issue with labels.txt and peakcall.tab
#372
tovahmarkowitz
closed
5 years ago
1
HPC snakemake upgrade incompatibility
#371
skchronicles
closed
5 years ago
1
Add ngsQC metrics
#370
tovahmarkowitz
closed
5 years ago
0
Add SV calling tools
#369
mtandon09
opened
5 years ago
0
scrna-next steps
#368
abdallahamr
closed
4 years ago
1
Create test datasets
#367
kopardev
opened
5 years ago
0
Create test datasets
#366
kopardev
closed
4 years ago
0
miRSeq - miRDeep2
#365
wong-nw
closed
5 years ago
0
Automate testing
#364
kopardev
opened
5 years ago
0
scrna implemented functions
#363
abdallahamr
closed
4 years ago
1
cutadapt
#362
kopardev
closed
5 years ago
0
Deeptools profile plots
#361
kopardev
closed
5 years ago
0
Deeptools heatmap
#360
kopardev
closed
5 years ago
0
Fingerplot
#359
kopardev
closed
5 years ago
0
Ability to Dynamically Resolve CCR BUY-NODES
#358
skchronicles
closed
5 years ago
1
RSEM CPM filtering (Master and module load)
#357
skchronicles
closed
5 years ago
1
updated splitNcigar GATK version to 3.8
#356
jlac
closed
5 years ago
0
reduced wall times and changed default partition to norm
#355
jlac
closed
5 years ago
0
Deeptools filenames resolving incorrectly (ChIP-seq)
#354
skchronicles
closed
5 years ago
1
GEO Upload Documentation
#353
skchronicles
closed
5 years ago
1
ChipSeq SE with filterdup
#352
kopardev
closed
5 years ago
0
repaired wgs_tumor_only bug in maftools
#351
jlac
closed
5 years ago
0
made theta2 outputs dynamic
#350
jlac
closed
5 years ago
0
reconfigured MAF filtering, added more MAF summaries, and added chronological prefix to hg38 chromosome names in haplotypecaller rules
#349
jlac
closed
5 years ago
0
split rnaseqvarcalling by chromosome
#348
jlac
closed
5 years ago
0
fixed bug in location of fusion STAR libraries
#347
jlac
closed
5 years ago
0
Initial ChIP-seq QC pipeline improvements
#346
tovahmarkowitz
closed
5 years ago
2
repaired fusion pipeline bugs, increased max jobs to 55, allowed one resubmission of failed jobs, split all haplotypecaller runs by chromosome
#345
jlac
closed
5 years ago
0
Reference Genome JSON file and RNA-seq Updates
#344
skchronicles
closed
5 years ago
1
updated STARfusion and Canvas versions; increased STARfusion multithreading; fixed WGS_somatic_tumor only bug
#343
jlac
closed
5 years ago
0
updated mm10 version of the snpeff reference genome
#342
jlac
closed
5 years ago
0
changed hg38 filter ExAC VCF
#341
jlac
closed
5 years ago
0
Issue #324
#340
kopardev
closed
5 years ago
1
updated hatplotype caller steps to GATK 3.8-0, fixed jdk inflater bug…
#339
jlac
closed
5 years ago
0
increased qualimap memory allocation and update canvas to most recent version to deal with known bug
#338
jlac
closed
5 years ago
0
ChIP-seq Multiqc Report: Samtools Flagstat and Fastq Screen Error
#337
skchronicles
closed
5 years ago
1
Removing old, out-dated documentation and updating github page links
#336
skchronicles
closed
5 years ago
1
RNA-seq Pipeline: Add Limma Voom Normalized Matrix with EBSeq Output
#335
skchronicles
closed
5 years ago
1
Issue #324
#334
kopardev
closed
5 years ago
0
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