koustav-pal

HiCBricks

HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.

feather

Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow

arrow

Apache Arrow is a columnar in-memory analytics layer designed to accelerate big data. It houses a set of canonical in-memory representations of flat and hierarchical data along with multiple language-bindings for structure manipulation. It also provides IPC and common algorithm implementations.

bioconda-recipes

Conda recipes for the bioconda channel.

ChIC

ChIC: ChIP-seq quality Control package

csen-marketing

data_challenge

distiller-nf

a modular Hi-C mapping pipeline

ember.js

Ember.js - A JavaScript framework for creating ambitious web applications

gexf-js

A JavaScript GEXF viewer

go

The Open Source Data Science Masters

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

HiC_tools

A collection of tools for Hi-C data analysis

homebrew-R-multiverse

jquery

jQuery JavaScript Library

juicebox

Software for visualizing data from Hi-C and other proximity mapping experiments

Juicebox-1

Visualization and analysis software for Hi-C data -

koustav-pal.github.io

MarkdownLight

Markdown syntax highlighting plugin and color scheme for Sublime Text 3

nf-core-hic-dsl2

nf-mappable-coverage

Mappable coverage computation from bed files

nfcore-circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

osxfuse

FUSE for OS X extends OS X by adding support for FUSE file systems

personal-puzzles

Some puzzles to keep my mind fresh

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

sigma.js

A JavaScript library dedicated to graph drawing

superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.

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

TCGAbarcode

upf1-kd-data-analysis