sameet

HiC-Pro

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

HiCPlotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

seurat

R toolkit for single cell genomics

ChIA-PET2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data

clipseqananalysis

cruzdb

python access to UCSC genomes database

DAseq

DoGFinder

EnrichedHeatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

generic_scripts

Generic scripts in different languages that will do only one thing properly.

quartoReport

Quarto Report for RNA-Seq differential gene expression analysis using DESeq2

scAnalysis

Repository to hold functions and code for single cell data analysis.

human_NETseq

kentUtils

UCSC command line bioinformatic utilities

R.4Cker

scExtras

seqtk

Toolkit for processing sequences in FASTA/Q formats

SingleCellWorkshop

SnakemakeRNASeqExample

An example RNAseq pipeline with snakemake on the NIH biowulf cluster

velocyto.R

RNA velocity estimation in R

VisCap

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data.

WESExplorer

Graphical explorer of the WES VCF files.