seqcode

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

6 followers
Penn State University, University Park, PA
http://mahonylab.org

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miniMDS miniMDS Public

Python 28 9
allo allo Public

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

Python 16 2
cross-species-domain-adaptation cross-species-domain-adaptation Public

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

Jupyter Notebook 11 6
sequnwinder sequnwinder Public

SeqUnwinder: a platform for deconvolving motifs associated with genomic labels

Java 7
chexmix chexmix Public

ChExMix: the ChIP-exo mixture model

Java 7
seqcode-core seqcode-core Public

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

Java 6 4

Repositories

pegr Public
Platform for Eukaryotic Genome Regulation

seqcode/pegr’s past year of commit activity

Groovy 3 MIT 1 38 (1 issue needs help) 0 Updated Jul 16, 2024
allo Public
Allo: a multi-mapped read rescue strategy for gene regulatory analyses

seqcode/allo’s past year of commit activity

Python 16 MIT 2 1 0 Updated Jul 14, 2024
seqchromloader Public
Provide ready-to-use dataloader for deep learning models

seqcode/seqchromloader’s past year of commit activity

Python 3 0 0 0 Updated Jul 9, 2024
miniMDS Public

seqcode/miniMDS’s past year of commit activity

Python 28 MIT 9 5 0 Updated Jun 30, 2024
Micro-C-Pipelines Public
This repository contains pipelines developed for processing Micro-C data

seqcode/Micro-C-Pipelines’s past year of commit activity

Python 0 1 0 0 Updated Jun 15, 2024
Bichrom-GAT-Scripts Public
Repository for Bichrom-GAT scripts

seqcode/Bichrom-GAT-Scripts’s past year of commit activity

Python 0 1 0 0 Updated May 25, 2024
chromdisco Public Forked from jmschrei/tfmodisco-lite
A fork of tfmodisco for chromatin interpretation

seqcode/chromdisco’s past year of commit activity

Python 0 MIT 15 0 0 Updated Apr 15, 2024
Bichrom-Regression Public Forked from seqcode/Bichrom
Transcription factor binding strength prediction by deep neural network

seqcode/Bichrom-Regression’s past year of commit activity

Python 1 MIT 4 0 0 Updated Feb 2, 2024
iFox-mES Public
UCSC trackhub links for Mahony lab iFox ChIP-exo analysis

seqcode/iFox-mES’s past year of commit activity

Python 1 MIT 1 0 0 Updated Sep 29, 2023
seqcode-core Public
SeqCode: Java code for the analysis of high-throughput sequencing data

seqcode/seqcode-core’s past year of commit activity

Java 6 MIT 4 0 0 Updated Sep 18, 2023