Kundaje Lab
Kundaje Lab
deeplift
Public facing deeplift repo
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
3DChromatin_ReplicateQC
Software to compute reproducibility and quality scores for Hi-C data
abstention
Algorithms for abstention, calibration and domain adaptation to label shift.
alzheimers_parkinsons
Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
ChromDragoNN
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"