madetunj Goto Github PK

chip-seq

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

docker-seaseq

converting seaseq to a docker image

docs

Documentation on St. Jude Cloud.

fithichip

Statistically Significant loops from HiChIP data

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

mignon

Mechanistic integrative analysis of RNA-Seq data

mtsg

Find and quantify COSMIC mutational signatures across samples

mytoil-cwl-101

Getting cwl workflow to work with Toil runner

peaksanno

Annotate the location of peaks in terms of important genomic features

pfastq-dump

parallel-fastq-dump implementation in bash script

pgap

NCBI Prokaryotic Genome Annotation Pipeline

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.

qcnext

qc metrics

reorg-dx-applet

dnanexus reorganization option: using your own applet

rnaindel

Somatic indel discovery tool for tumor RNA-Seq data.

seacr

SEACR: Sparse Enrichment Analysis for CUT&RUN

seaseq-dev

development of seaseq

seaseq-docker-dev

seaseq as a docker image

sicer2

test_toil

testing toil installation

transatlasdb

TransAtlasDB: an informatics system for transcriptome analysis data

university

Educational materials for the St. Jude Cloud project.

wdl-seaseq

workflows

Community maintained workflows & tools (with examples)