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bioinformatics

Bioinformatics analysis scripts, workflows, general code examples

bowtie2

A fast and sensitive gapped read aligner

c.origami-jrh_model

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

chipseeker

:dart:ChIP peak Annotation, Comparison and Visualization

cnv-nf

cnvkit

Copy number variant detection from targeted DNA sequencing

conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays -

datasharing

The Leek group guide to data sharing

dbind

deepbind

Training and testing of DeepBind models.

deeptools

Tools to process and analyze deep sequencing data.

deseq2

Differential gene expression analysis based on the negative binomial distribution

development

Tools and guides in production

diff-boundaries

A pipeline to perform a pairwise differential analysis of TAD boundary insulation in two conditions

diffbind

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/DiffBind.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=DiffBind.

fimo

fix-bam-header

genomics

a collection of scripts and notes related to genomics and bioinformatics

hic-bench

A set of pipelines for Hi-C and ChIP-Seq analysis.

hic-bench_documentation

User manuals for the HiC-Bench software

homer

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

juicebox

Visualization and analysis software for Hi-C data -

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

limma

A github copy of limma package from Bioconductor

macs

MACS -- Model-based Analysis of ChIP-Seq

masters

maxatac

methylkit

R package for DNA methylation analysis

minfi

Devel repository for minfi