13 open source projects by kundajelab

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

ATAC-seq and DNase-seq processing pipeline

AQUAS TF and histone ChIP-seq pipeline

Public facing deeplift repo

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

Deep Feature Interaction Maps (DFIM)

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)

Simple and efficient access to genomic data for deep learning models.

A python library for creating simulated regulatory DNA sequences

IDR

Downloader for ENCODE