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bamfix

Strip /1 and /2 from BAM QNAME fields

chkcghub

Python script to check the existence, size, and checksum of files downloaded from the Cancer Genomics Hub (CGHub)

diffmotif

R tools for differential analysis of motif patterns

dptmethods

R package provides support to dptscan software pipeline

dptscan

Analysis pipeline for genome-wide de novo identification of differential enrichment events from next generation sequencing data

dptviz

Visualize differentially methylated regions detected by iDPT

gencon

Output genomic context for a BED file of genomic ranges

genomesyncr

R package to sync and parse UCSC Genome Browser table data

goldmine

Annotate genomic contexts and discover functional element enrichments

handy

Handy R Functions

jeffbhasin.github.io

Documentation website for the Goldmine and MethylAction projects

methylaction

Differentially Methylated Regions (DMRs) from MBD-isolated Genome Sequencing (MiGS/MBD-seq)

methylaction_demo

Demo for the MethylAction R Package

pyfaidx

pyfaidx: efficient pythonic random access to fasta subsequences

rtcga

snpscope

Compute overlap of SNPs with regulatory elements and export to CSV or the UCSC Genome Browser