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hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hickry

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

hicnv

HiCnv is used to call copy number variations and breakpoints from Hi-C data

hictrans

HiCtrans is a pipeline to call translocations from Hi-C data

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

iqtl

Interaction QTL (IQTL) using HiChIP contacts

karyoploter

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

klib

A standalone and lightweight C library

lji_rna_seq_pipeline_v2

Snakemake based RNA-Seq QC pipeline for cloud/cluster implementation

lji_rna_seq_qc_pipeline_v1

mio

Cross-platform C++11 header-only library for memory mapped file IO

miso

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

mustache

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

pieqtl_ng

pytorch-vae

A Collection of Variational Autoencoders (VAE) in PyTorch.

rna_seq_pipeline

RNA-seq data processing and QC

s_ldsc_snp

Stratified LD score regression analysis

selfish

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

sip

SIP: Significant Interaction Peak caller

sldp

Signed LD profile regression

sle-mwgcna

Multi-cell type gene co-expression network analysis reveals coordinated interferon response and cross cell-type correlations in SLE

sra-explorer

Web application to explore the Sequence Read Archive.

straw

Extract data quickly from Juicebox via straw

tools

A collection of command-line tools I wrote to make various repetitive tasks more convenient

utilities

Various utility scripts for 3C data analysis