seqcode

Collection of projects related to DNA sequencing data processing & regulatory genomics analyses

Penn State University, University Park, PA

Pinned Repositories

allo
Allo: a multi-mapped read rescue strategy for gene regulatory analyses
Language:Python22 5 32
Bichrom
Interpretable bimodal network for transcription factors binding site prediction
Language:Python6 5 24
chexmix
ChExMix: the ChIP-exo mixture model
Language:Java7 3 70
chromosom
ChromoSOM: a Self-Organizing Map for analyzing chromatin interactions
Language:Java3 2 11
cross-species-domain-adaptation
Codebase for the domain adaptation (cross-species TF binding prediction) project.
Language:Jupyter Notebook11 3 66
IDEAS
Jointly characterizing epigenetic dynamics across multiple cell types
Language:C++6 2 02
miniMDS
Language:Python29 4 299
seqcode-core
SeqCode: Java code for the analysis of high-throughput sequencing data
Language:Java6 3 04
sequnwinder
SeqUnwinder: a platform for deconvolving motifs associated with genomic labels
Language:Java7 5 20
stamp
STAMP
Language:C++3 3 12

seqcode's Repositories

seqcode/miniMDS
Language:Python29 4 299
seqcode/allo
Allo: a multi-mapped read rescue strategy for gene regulatory analyses
Language:Python22 5 32
seqcode/cross-species-domain-adaptation
Codebase for the domain adaptation (cross-species TF binding prediction) project.
Language:Jupyter Notebook11 3 66
seqcode/chexmix
ChExMix: the ChIP-exo mixture model
Language:Java7 3 70
seqcode/sequnwinder
SeqUnwinder: a platform for deconvolving motifs associated with genomic labels
Language:Java7 5 20
seqcode/Bichrom
Interpretable bimodal network for transcription factors binding site prediction
Language:Python6 5 24
seqcode/seqcode-core
SeqCode: Java code for the analysis of high-throughput sequencing data
Language:Java6 3 04
seqcode/cegr-galaxy
CEGR proprietary Galaxy components: pre-processing pipeline, ChIP-exo statistics tools, etc.
Language:Python3 6 12
seqcode/chromosom
ChromoSOM: a Self-Organizing Map for analyzing chromatin interactions
Language:Java3 2 11
seqcode/multigps
MultiGPS: software for analyzing collections of multi-condition ChIP-seq datasets
Language:Java3 2 22
seqcode/pegr
Platform for Eukaryotic Genome Regulation
Language:Groovy3 5 2671
seqcode/seqchromloader
Provide ready-to-use dataloader for deep learning models
Language:Python3 2 00
seqcode/stamp
STAMP
Language:C++3 3 12
seqcode/chexalign
ChExAlign: alignment and quantification of ChIP-exo crosslinking patterns
Language:Java2 4 1
seqcode/Bichrom-Regression
Transcription factor binding strength prediction by deep neural network
Language:Python1 0 0
seqcode/cegr-tools
A set of utilities for use in the ChIP-exo flavor of Galaxy
Language:Java1 5 10
seqcode/iFox-mES
UCSC trackhub links for Mahony lab iFox ChIP-exo analysis
Language:Python1 1 01
seqcode/multimds
Language:Python1 3 1
seqcode/Bichrom-GAT-Scripts
Repository for Bichrom-GAT scripts
Language:Python0 1 01
seqcode/Micro-C-Pipelines
This repository contains pipelines developed for processing Micro-C data
Language:Python0 1 01
seqcode/pegr-docker
Language:Dockerfile0 3 00
seqcode/seqview-web-docker-public
Wrapper for existing genome browsers to search for files based on their metadata.
Language:Python0 3 01
seqcode/chromdisco
A fork of tfmodisco for chromatin interpretation
Language:Python0 0
seqcode/domain_adaptive_nn
Cross-species TF binding prediction
Language:Jupyter Notebook1 0
seqcode/igv-webapp-embeddable
IGV Web App
Language:JavaScript1 21
seqcode/mazzoni-zbtb-trackhub
Trackhub for Mazzoni lab mES ZBTB ChIP-seq tracks
Language:HTML2 0
seqcode/multispecies-domain-adaptation
Language:Python2 0
seqcode/shap-hypothetical
A game theoretic approach to explain the output of any machine learning model.
Language:Jupyter Notebook0 0
seqcode/WaveNet
Yet another WaveNet implementation in PyTorch.
Language:Python0 0
seqcode/yep-trackhubs
UCSC genome browser trackhubs for YEP project
Language:HTML2 0