ay-lab/ATACProc ay-lab/ATACProc

  • Stars
    star
    30
  • Rank 839,658 (Top 17 %)
  • Language
    Shell
  • Created over 6 years ago
  • Updated over 2 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
ay-lab/ATACProc
github

ay-lab

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

ATAC-seq processing pipeline

More Repositories

1

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.
Python
79
star
2

mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Python
62
star
3

dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
R
56
star
4

FitHiChIP

Statistically Significant loops from HiChIP data
R
38
star
5

HiCnv

HiCnv is used to call copy number variations and breakpoints from Hi-C data
Python
21
star
6

selfish

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.
Python
17
star
7

HiCtrans

HiCtrans is a pipeline to call translocations from Hi-C data
R
15
star
8

ExTraMapper

ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequence conservation.
Python
9
star
9

Colocalization

Co-localization analysis between reference GWAS and eQTL summary statistics
R
8
star
10

ChIPLine

ChIP-seq analysis pipeline
Shell
8
star
11

AveSim

AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.
Perl
5
star
12

3D-IKAROS

Utility scripts related to IKAROS manuscript
R
3
star
13

IQTL

Interaction QTL (IQTL) using HiChIP contacts
R
3
star
14

S_LDSC_SNP

Stratified LD score regression analysis
Shell
3
star
15

GhmCN

Graphical 5hmC Convolutional Networks
Python
2
star
16

Utilities

Various utility scripts for 3C data analysis
R
2
star
17

pieQTL_NG

R
2
star
18

dcHiCviz

Visualization for dcHiC files.
HTML
1
star
19

Brd2_analysis

Analysis and data from report titled 'Brd2 is dispensable for genome compartmentalization and replication timing'
HTML
1
star
20

FineMap

R
1
star
21

HiCKRy

HiCKRy is a tool developed by the Ay Lab to normalize HiC data using the Knight-Ruiz algorithm for matrix normalization.
Python
1
star