Aiden Lab

Aiden Lab's repositories

juicer

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

Language:ShellMIT399 17 304

Juicebox

Visualization and analysis software for Hi-C data -

Language:JavaMIT233 23 822

3d-dna

3D de novo assembly (3D DNA) pipeline

Language:ShellMIT196 13 181

straw

Extract data quickly from Juicebox via straw

Language:C++MIT61 11 65

JuiceboxLegacy

OLD REPOSITORY - Go to

Language:JavaMIT32 12 14

JuicerTools

Language:JavaMIT11 7 3

BEAR

BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

Language:ShellMIT7 9 3

EigenVector

R functions for very fast eigenvector calculation

Language:C7 10

JuiceboxGUI

Language:JavaMIT5 7 1

welcome

Getting started with Hi-C data analysis

Language:HTMLMIT4 60

HiCTools

Language:JavaMIT3 70

JuiceMe

Hi-Culfite Processing Pipeline

Language:ShellMIT3 80

hic-format

2 90

pyStraw

Python only flavor of straw for streaming .hic data [Deprecated]

Language:Jupyter NotebookMIT2 60

MDsimulations

Simulation code

Language:PythonMIT1 50

3d-carta

Language:ShellMIT050

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

Language:PostScriptMIT010

clear-tools

Chromatin Landscape Exploration, Analysis, and Research Tools

Language:JavaMIT000

contact-probability

Updated Adrian's code

Language:Python02 1

hic2gatk

Language:ShellMIT060

java-straw

Language:JavaMIT010

juicebox.js

HiC contact matrix visualization

Language:JavaScriptMIT020

JuiceboxReader

[Deprecated] Fast reading/dump for .hic files

Language:C++MIT04 2

juicer_old

Aiden Lab old version of Juicer, for archival purposes

Language:Python040

mcph1_notebook

Language:Jupyter NotebookMIT060

mmba

Moshe's matrix balancing algorithm

Language:C09 3

PAP

Language:Shell000

welcome-images

050