madetunj

Pinned Repositories

ChIP-Seq
Language:Python0 1 00
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python0 1 00
docker-seaseq
converting seaseq to a docker image
Language:Dockerfile0 2 00
docs
Documentation on St. Jude Cloud.
Language:Shell00
FitHiChIP
Statistically Significant loops from HiChIP data
Language:R0 0 00
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Language:Python0 0 00
MIGNON
Mechanistic integrative analysis of RNA-Seq data
Language:WDL00
mtsg
Find and quantify COSMIC mutational signatures across samples
Language:Python00
myToil-CWL-101
Getting cwl workflow to work with Toil runner
Language:Shell0 2 00
peaksanno
Annotate the location of peaks in terms of important genomic features
Language:Python1 2 00

madetunj's Repositories

madetunj/peaksanno
Annotate the location of peaks in terms of important genomic features
Language:Python1 2 00
madetunj/ChIP-Seq
Language:Python0 1 00
madetunj/chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python0 1 00
madetunj/docker-seaseq
converting seaseq to a docker image
Language:Dockerfile0 2 00
madetunj/docs
Documentation on St. Jude Cloud.
Language:Shell00
madetunj/FitHiChIP
Statistically Significant loops from HiChIP data
Language:R0 0 00
madetunj/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Language:Python0 0 00
madetunj/MIGNON
Mechanistic integrative analysis of RNA-Seq data
Language:WDL00
madetunj/mtsg
Find and quantify COSMIC mutational signatures across samples
Language:Python00
madetunj/myToil-CWL-101
Getting cwl workflow to work with Toil runner
Language:Shell0 2 00
madetunj/pfastq-dump
parallel-fastq-dump implementation in bash script
Language:Shell1 0
madetunj/pgap
NCBI Prokaryotic Genome Annotation Pipeline
Language:Common Workflow Language
madetunj/phantompeakqualtools-public
This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
Language:R
madetunj/QCNext
qc metrics
Language:R
madetunj/reorg-dx-applet
dnanexus reorganization option: using your own applet
Language:Python2 0
madetunj/RNAIndel
Somatic indel discovery tool for tumor RNA-Seq data.
Language:Python0 0
madetunj/SEACR
SEACR: Sparse Enrichment Analysis for CUT&RUN
madetunj/seaseq-dev
development of seaseq
Language:Common Workflow Language2 01
madetunj/seaseq-docker-dev
seaseq as a docker image
Language:Dockerfile
madetunj/SICER2
madetunj/test_toil
testing toil installation
Language:Common Workflow Language2 0
madetunj/TransAtlasDB
TransAtlasDB: an informatics system for transcriptome analysis data
Language:HTML1 0
madetunj/university
Educational materials for the St. Jude Cloud project.
Language:JavaScript1 0
madetunj/wdl-seaseq
Language:WDL1 0
madetunj/workflows
Community maintained workflows & tools (with examples)
Language:Common Workflow Language1 0