seqcode

miniMDS

allo

Allo: a multi-mapped read rescue strategy for gene regulatory analyses

cross-species-domain-adaptation

Codebase for the domain adaptation (cross-species TF binding prediction) project.

chexmix

ChExMix: the ChIP-exo mixture model

sequnwinder

SeqUnwinder: a platform for deconvolving motifs associated with genomic labels

Bichrom

Interpretable bimodal network for transcription factors binding site prediction

seqcode-core

SeqCode: Java code for the analysis of high-throughput sequencing data

cegr-galaxy

CEGR proprietary Galaxy components: pre-processing pipeline, ChIP-exo statistics tools, etc.

chromosom

ChromoSOM: a Self-Organizing Map for analyzing chromatin interactions

multigps

MultiGPS: software for analyzing collections of multi-condition ChIP-seq datasets

pegr

Platform for Eukaryotic Genome Regulation

seqchromloader

Provide ready-to-use dataloader for deep learning models

stamp

STAMP

chexalign

ChExAlign: alignment and quantification of ChIP-exo crosslinking patterns

Bichrom-Regression

Transcription factor binding strength prediction by deep neural network

cegr-tools

A set of utilities for use in the ChIP-exo flavor of Galaxy

iFox-mES

UCSC trackhub links for Mahony lab iFox ChIP-exo analysis

multimds

pegr-docker

seqview-web-docker-public

Wrapper for existing genome browsers to search for files based on their metadata.

Bichrom-GAT-Scripts

Repository for Bichrom-GAT scripts

chromdisco

A fork of tfmodisco for chromatin interpretation

domain_adaptive_nn

Cross-species TF binding prediction

igv-webapp-embeddable

IGV Web App

mazzoni-zbtb-trackhub

Trackhub for Mazzoni lab mES ZBTB ChIP-seq tracks

Micro-C-Pipelines

This repository contains pipelines developed for processing Micro-C data

multispecies-domain-adaptation

shap-hypothetical

A game theoretic approach to explain the output of any machine learning model.

WaveNet

Yet another WaveNet implementation in PyTorch.

yep-trackhubs

UCSC genome browser trackhubs for YEP project