seqcode/Aydin_2019_iAscl1-vs-iNeurog2

Stars
2
Language
Shell
Created almost 6 years ago
Updated almost 6 years ago

seqcode/Aydin_2019_iAscl1-vs-iNeurog2

seqcode

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

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

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.

Jupyter Notebook

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

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