seqcode/cross-species-domain-adaptation

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seqcode/cross-species-domain-adaptation

seqcode

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

miniMDS

allo

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

sequnwinder

SeqUnwinder: a platform for deconvolving motifs associated with genomic labels

chexmix

ChExMix: the ChIP-exo mixture model

Bichrom

Interpretable bimodal network for transcription factors binding site prediction

seqcode-core

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

stamp

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

cegr-galaxy

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

seqchromloader

Provide ready-to-use dataloader for deep learning models

chexalign

ChExAlign: alignment and quantification of ChIP-exo crosslinking patterns

Aydin_2019_iAscl1-vs-iNeurog2

Contains analysis scripts used to process data for Aydin, et al. 2019 manuscript

cegr-tools

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

encodedream

Code for our contribution to the ENCODE/DREAM challenge

multimds

pyseqcode

pyseqcode: Python code for the analysis of high-throughput sequencing data

iFox-mES

UCSC trackhub links for Mahony lab iFox ChIP-exo analysis