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beta

Binding and Expression Target Analysis pipeline

bioconda-recipes

Conda recipes for the bioconda channel.

deeptools

Tools to process and analyze deep sequencing data.

giniclust

GiniClust: Detecting Rare Cell Types from Single-Cell Gene Expression Data with Gini Index

hic_pipeline

A user-friendly Hi-C data processing software based on hiclib

hint

HiC for copy Number variation and Translocation detection

hint-sv-explorer

iced

Normalizing Hi-C contact counts efficiently

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

marge

MARGE:Model-based Analysis of Regulation of Gene Expression

marge_py2

MARGE:Model-based Analysis of Regulation of Gene Expression (for python2)

marge_py3

MARGE:Model-based Analysis of Regulation of Gene Expression (for python3)

tadbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models