Kundaje Lab

dragonn

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

tfmodisco

TF MOtif Discovery from Importance SCOres

chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

simdna

A python library for creating simulated regulatory DNA sequences

idr

IDR

basepairmodels

Cardiogenesis_Repo

Cardiogenesis Repo

variant-scorer

A framework to score and analyze variant effects genome-wide using ChromBPNet models

ENCODE_scatac

scATAC-reprog

Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.

coessentiality-browser

Gene browser using coessentiality and related data

dynseq-pages

nascent_RNA_models

Repository for modeling PRO-cap data with BPNet.

bpnet-refactor

affinity_distillation

chrombench

jamboree-toolkit

toolkit for setting up compute environment on gcp for jamborees

SVM_pipelines

anvil-variant-scoring

atacseq-dnaseseq-chrombpnet-modelzoo-pipeline

dynseq-paper

ENCODE_manual_adrenal

ENCODE_manual_liver

encode_upload_tfatlas_readmes

hitcallerNet

humbio51-student

student files for humbio51

ProCapNet

Repository for ProCapNet models for learning the cis-regulatory syntax of transcription initiation.

procapnet-modelzoo-pipeline

Repository for the pipeline to run ProCapNet.

synapse-backup-syncer

Create and sync backups to Synapse

track-hubs