Kundaje Lab
Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.
Stanford University
Pinned Repositories
3DChromatin_ReplicateQC
Software to compute reproducibility and quality scores for Hi-C data
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
deeplift
Public facing deeplift repo
dfim
Deep Feature Interaction Maps (DFIM)
dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
phantompeakqualtools
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.
tfmodisco
TF MOtif Discovery from Importance SCOres
Kundaje Lab's Repositories
kundajelab/dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
kundajelab/bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
kundajelab/chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
kundajelab/tfmodisco
TF MOtif Discovery from Importance SCOres
kundajelab/simdna
A python library for creating simulated regulatory DNA sequences
kundajelab/idr
IDR
kundajelab/basepairmodels
kundajelab/DART-Eval
kundajelab/ProCapNet
Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
kundajelab/Cardiogenesis_Repo
Cardiogenesis Repo
kundajelab/ENCODE_scatac
kundajelab/variant-scorer
A framework to score and analyze variant effects genome-wide using ChromBPNet models
kundajelab/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.
kundajelab/ImmuneCLIP
Repository for code and data related to ImmuneCLIP
kundajelab/bpnet-refactor
kundajelab/affinity_distillation
kundajelab/CTCFMutants
kundajelab/jamboree-toolkit
toolkit for setting up compute environment on gcp for jamborees
kundajelab/retina-design
Designing AAV sequences for retinal cell types (with scATAC-seq models)
kundajelab/TENet
kundajelab/encode_upload_tfatlas_readmes
kundajelab/anvil-variant-scoring
kundajelab/atacseq-dnaseseq-chrombpnet-modelzoo-pipeline
kundajelab/ENCODE_manual_adrenal
kundajelab/ENCODE_manual_liver
kundajelab/hitcallerNet
kundajelab/humbio51-student
student files for humbio51
kundajelab/procapnet-modelzoo-pipeline
Repository for the pipeline to run ProCapNet.
kundajelab/synapse-backup-syncer
Create and sync backups to Synapse
kundajelab/track-hubs