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a_thaliana_epigenetic_mutants

accost

Differentional Hi-C contact count statistics

as_analysis

chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

cls_rice

comm-methylation

This repo is to collect the FAANG methylation group's code and pipelines

coolbox

Jupyter notebook based genomic data visualization toolkit.

cooler

A cool place to store your Hi-C

cooltools

The tools for your .cool's

fanc

FAN-C: Framework for the ANalysis of C-like data

feelnc

FEELnc : FlExible Extraction of LncRNA

fithic

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

geneneighborhood

Analyze the neighborhood (upstream/downstream neighbors) of any gene set

genova

GENome Organisation Visual Analytics

hic_tools

A collection of tools for Hi-C data analysis

hicassembler

Software to assemble contigs/scaffolds into chromosomes using Hi-C data

hicorr

HiCorr: a Hi-C data bias-correction pipeline

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

higlass

Fast, flexible and extensible genome browser.

icount

iCount, protein-RNA interaction analytics

ihic

A set of C++ utilities for data pre/post-procession to faciliate Hi-C data analysis with public software

local-compartment

R script for local compartment calling

metacluster

R package for context-specific functionality analysis of metabolic gene clusters

motifsearcher

Here, we describe and provide an RNA-Seq analysis of a RIP assay to understand the mechanism of AML del(9q) progression.

pareidolia

Multi-sample change detection in Hi-C patterns

piranha

Piranha is a peak-caller for CLIP- and RIP-seq data

plant-bs-seq-analysis

Whole-Genome Bisulfite Sequencing (BS-Seq) Bioinformatic analysis

population_genetics

Start to Test Pop gen on BIG DATA

pygenometracks

python module to plot beautiful and highly customizable genome browser tracks

q_lncrna_analysis