kundajelab/phantompeakqualtools

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kundajelab/phantompeakqualtools

kundajelab

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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.

deeplift

Public facing deeplift repo

dragonn

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

Jupyter Notebook

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

Jupyter Notebook

tfmodisco

TF MOtif Discovery from Importance SCOres

Jupyter Notebook

chrombpnet

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

Jupyter Notebook

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

dfim

Deep Feature Interaction Maps (DFIM)

ChromDragoNN

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

Jupyter Notebook

3DChromatin_ReplicateQC

Software to compute reproducibility and quality scores for Hi-C data

alzheimers_parkinsons

Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

Jupyter Notebook

genomelake

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

simdna

A python library for creating simulated regulatory DNA sequences

abstention

Algorithms for abstention, calibration and domain adaptation to label shift.

coda

Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data

cs273b

CS273B Deep Learning for Genomics Course Materials

Jupyter Notebook

ENCODE_downloader

Downloader for ENCODE

coessentiality

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

genomedisco

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

Jupyter Notebook

training_camp

Genetics training camp

Jupyter Notebook

gkmexplain

Accompanying repository for GkmExplain paper

Jupyter Notebook

fastISM

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

Jupyter Notebook

ataqc

basepairmodels

labelshiftexperiments

Label shift experiments

Jupyter Notebook

seqdataloader

Sequence data label generation and ingestion into deep learning models

bpnet-manuscript

BPNet manuscript code.

Jupyter Notebook

higlass-dynseq

Dynamic sequence track for HiGlass

DeepBindToKeras

Convert DeepBind models to Keras

ProCapNet

Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.

Jupyter Notebook

MPRA-DragoNN

Code accompanying the paper "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays"

mpra

Deep learning MPRAs

Jupyter Notebook

ENCODE_scatac

variant-scorer

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

tronn

Transcriptional Regulation (Optimized) Neural Nets (TRoNN)

Cardiogenesis_Repo

Cardiogenesis Repo

Jupyter Notebook

deepbind

I have put my modified version of the deepbind code here.

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.

Jupyter Notebook

veryolddontuse_deeplift_modisco_tutorial

Jupyter Notebook

chromovar3d

Code from the chromatin variation 3d project

chip-nexus-pipeline

ChIP-nexus pipeline

kerasAC

keras accessibility models: code to train, predict, interpret

DART-Eval

Jupyter Notebook

DMSO

Jupyter Notebook

mesoderm

Scripts for dataset processing and QC for the mesoderm differentiation project.

1kg_ld_utils

utils/notes for LD calculation from 1000 genomes panel

keras-genomics

Genomics layers for Keras 2

lsgkm-svr

lsgkm+gkmexplain with regression functionality. Builds off kundajelab/lsgkm (which has gkmexplain), which in turn builds off Dongwon-Lee/lsgkm (the original lsgkm repo)

yuzu

yuzu is a compressed-sensing based approach for quickly calculating in-silico mutagenesis saliency.

PFBoost

modular 2D boosting code with stabilization and hierarchies

coessentiality-browser

Gene browser using coessentiality and related data

zenodo_upload

Python script to upload files to Zenodo

neural_motif_discovery

Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations

Jupyter Notebook

vizsequence

Collecting commonly-repeated sequence visualization code here

av_scripts

A place to track my scripts with git.

Jupyter Notebook

bpnet-refactor

dynseq-pages

locusselect

extraction of data embeddings from deep learning model layers; computation of embedding distance and visualization with umap/tsne

Jupyter Notebook

atlas_resources

A nucleotide-resolution, context-specific sequence annotation of the dynamic regulatory landscape of the human and mouse genomes

tf_binding_challenge

scoring/ranking code for tf binding challenge

bulk-rna-seq

Pipeline for gecco RNA-seq analysis

python_reading_group

Jupyter Notebook

higlass-multi-tileset

Multi-tileset data fetcher for HiGlass

retina-models

BPNet models for retina single-cell multiome data

Jupyter Notebook

TF-Atlas

Code repository for the TF-Atlas project

Jupyter Notebook

crispr_safe_targeting_regions

Repository for creating the CRISPR controls termed "safe harbor" regions from Morgens et al., 2017, Nat Comms.

interpret-benchmark

Benchmarking interpretation methods

Jupyter Notebook

kCCA

momma_dragonn

Flexible deep learning framework

Jupyter Notebook

feature_interactions

Jupyter Notebook

bds_pipeline_modules

BigDataScript (BDS) pipelines and modules

mseqgen

Multi task batch generator for training deep learning models on CHIP-seq, CHIP-exo, CHIP-nexus, ATAC-seq, RNA-seq (or any other -seq)

SVM_pipelines

Jupyter Notebook

jamboree-toolkit

toolkit for setting up compute environment on gcp for jamborees

genomics-DL-archsandlosses

A collection of Deep Learning architectures and loss functions from across the genomics literature

affinity_distillation

Jupyter Notebook

SeqPriorizationCATLAS

Sequence priorization using gkm-explain.

Jupyter Notebook

chromBPNet-tutorial

How to train BPNets on ATAC-seq data using the Basepairmodels repo from Stanford's Kundaje Lab.

PREUSS

PREUSS: predicting RNA editing using sequence and structure

Jupyter Notebook

CTCFMutants

Jupyter Notebook