Repositories list

• seqaffinity

  Public

  seqcode/seqaffinity’s past year of commit activity
  Jupyter Notebook

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  MIT License

  •00 forks in seqcode/seqaffinity•00 stars in seqcode/seqaffinity•00 issues in seqcode/seqaffinity•00 pull requests in seqcode/seqaffinity•Updated Oct 18, 2026Oct 18, 2026

• pegr

  Public

  seqcode/pegr’s past year of commit activity
  Platform for Eukaryotic Genome Regulation

  Groovy

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  MIT License

  •11 fork in seqcode/pegr•44 stars in seqcode/pegr•3838 issues in seqcode/pegr•00 pull requests in seqcode/pegr•Updated Sep 17, 2026Sep 17, 2026

• stamp

  Public

  seqcode/stamp’s past year of commit activity
  STAMP

  TypeScript

  •33 forks in seqcode/stamp•55 stars in seqcode/stamp•11 issue in seqcode/stamp•00 pull requests in seqcode/stamp•Updated Aug 28, 2026Aug 28, 2026

• TPCAV

  Public

  seqcode/TPCAV’s past year of commit activity
  Testing with PCA projected Concept Activation Vectors

  Jupyter Notebook

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  MIT License

  •00 forks in seqcode/TPCAV•33 stars in seqcode/TPCAV•00 issues in seqcode/TPCAV•00 pull requests in seqcode/TPCAV•Updated Aug 26, 2026Aug 26, 2026

• ncems-simplified

  Public

  seqcode/ncems-simplified’s past year of commit activity
  Simplified ENCODE processing pipelines for ChIP-seq and ATAC-seq, incorporating Allo

  Python

  •00 forks in seqcode/ncems-simplified•00 stars in seqcode/ncems-simplified•00 issues in seqcode/ncems-simplified•00 pull requests in seqcode/ncems-simplified•Updated Aug 10, 2026Aug 10, 2026

• bioinformatics-educational-react-apps

  Public

  seqcode/bioinformatics-educational-react-apps’s past year of commit activity
  A collection of educational bioinformatics apps that illustrate bioinformatics algorithms

  HTML

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  MIT License

  •00 forks in seqcode/bioinformatics-educational-react-apps•00 stars in seqcode/bioinformatics-educational-react-apps•00 issues in seqcode/bioinformatics-educational-react-apps•00 pull requests in seqcode/bioinformatics-educational-react-apps•Updated Jul 21, 2026Jul 21, 2026

• seqchromloader

  Public

  seqcode/seqchromloader’s past year of commit activity
  Provide ready-to-use dataloader for deep learning models

  Python

  •00 forks in seqcode/seqchromloader•33 stars in seqcode/seqchromloader•00 issues in seqcode/seqchromloader•00 pull requests in seqcode/seqchromloader•Updated Jul 7, 2026Jul 7, 2026

• chexmix

  Public
  ChExMix: the ChIP-exo mixture model

  Java

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  MIT License

  •11 fork in seqcode/chexmix•77 stars in seqcode/chexmix•44 issues in seqcode/chexmix•00 pull requests in seqcode/chexmix•Updated Oct 24, 2025Oct 24, 2025

• seqcode-core

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

  Java

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  MIT License

  •44 forks in seqcode/seqcode-core•66 stars in seqcode/seqcode-core•00 issues in seqcode/seqcode-core•00 pull requests in seqcode/seqcode-core•Updated Jul 18, 2025Jul 18, 2025

• pfal-chrom-states-trackhub

  Public
  Plasmodium falciparum chromatin state trackhubs for UCSC genome browser

  Python

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  MIT License

  •00 forks in seqcode/pfal-chrom-states-trackhub•00 stars in seqcode/pfal-chrom-states-trackhub•00 issues in seqcode/pfal-chrom-states-trackhub•00 pull requests in seqcode/pfal-chrom-states-trackhub•Updated May 23, 2025May 23, 2025

• allo

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

  Python

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  MIT License

  •55 forks in seqcode/allo•2525 stars in seqcode/allo•00 issues in seqcode/allo•00 pull requests in seqcode/allo•Updated Sep 5, 2024Sep 5, 2024

• miniMDS

  Public
  Python

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  MIT License

  •99 forks in seqcode/miniMDS•3131 stars in seqcode/miniMDS•55 issues in seqcode/miniMDS•00 pull requests in seqcode/miniMDS•Updated Jun 30, 2024Jun 30, 2024

• Micro-C-Pipelines

  Public
  This repository contains pipelines developed for processing Micro-C data

  Python

  •11 fork in seqcode/Micro-C-Pipelines•22 stars in seqcode/Micro-C-Pipelines•00 issues in seqcode/Micro-C-Pipelines•00 pull requests in seqcode/Micro-C-Pipelines•Updated Jun 15, 2024Jun 15, 2024

• Bichrom-GAT-Scripts

  Public
  Repository for Bichrom-GAT scripts

  Python

  •11 fork in seqcode/Bichrom-GAT-Scripts•00 stars in seqcode/Bichrom-GAT-Scripts•00 issues in seqcode/Bichrom-GAT-Scripts•00 pull requests in seqcode/Bichrom-GAT-Scripts•Updated May 25, 2024May 25, 2024

• chromdisco

  Public
  A fork of tfmodisco for chromatin interpretation

  Python

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  MIT License

  •2626 forks in seqcode/chromdisco•00 stars in seqcode/chromdisco•00 issues in seqcode/chromdisco•00 pull requests in seqcode/chromdisco•Updated Apr 15, 2024Apr 15, 2024

• Bichrom-Regression

  Public
  Transcription factor binding strength prediction by deep neural network

  Python

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  MIT License

  •33 forks in seqcode/Bichrom-Regression•11 star in seqcode/Bichrom-Regression•00 issues in seqcode/Bichrom-Regression•00 pull requests in seqcode/Bichrom-Regression•Updated Feb 2, 2024Feb 2, 2024

• iFox-mES

  Public

  seqcode/iFox-mES’s past year of commit activity
  UCSC trackhub links for Mahony lab iFox ChIP-exo analysis

  Python

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  MIT License

  •22 forks in seqcode/iFox-mES•11 star in seqcode/iFox-mES•00 issues in seqcode/iFox-mES•00 pull requests in seqcode/iFox-mES•Updated Sep 29, 2023Sep 29, 2023

• Bichrom

  Public
  Interpretable bimodal network for transcription factors binding site prediction

  Python

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  MIT License

  •33 forks in seqcode/Bichrom•1010 stars in seqcode/Bichrom•00 issues in seqcode/Bichrom•00 pull requests in seqcode/Bichrom•Updated Jun 29, 2023Jun 29, 2023

• mazzoni-zbtb-trackhub

  Public
  Trackhub for Mazzoni lab mES ZBTB ChIP-seq tracks

  HTML

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  MIT License

  •00 forks in seqcode/mazzoni-zbtb-trackhub•00 stars in seqcode/mazzoni-zbtb-trackhub•00 issues in seqcode/mazzoni-zbtb-trackhub•00 pull requests in seqcode/mazzoni-zbtb-trackhub•Updated Feb 10, 2023Feb 10, 2023

• seqview-web-docker-public

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

  Python

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  MIT License

  •11 fork in seqcode/seqview-web-docker-public•00 stars in seqcode/seqview-web-docker-public•00 issues in seqcode/seqview-web-docker-public•00 pull requests in seqcode/seqview-web-docker-public•Updated Jan 27, 2023Jan 27, 2023

• shap-hypothetical

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

  Jupyter Notebook

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  MIT License

  •3.8k3.8k forks in seqcode/shap-hypothetical•00 stars in seqcode/shap-hypothetical•00 issues in seqcode/shap-hypothetical•00 pull requests in seqcode/shap-hypothetical•Updated Jan 25, 2023Jan 25, 2023

• WaveNet

  Public
  Yet another WaveNet implementation in PyTorch.

  Python

  •2929 forks in seqcode/WaveNet•00 stars in seqcode/WaveNet•00 issues in seqcode/WaveNet•00 pull requests in seqcode/WaveNet•Updated Jan 4, 2023Jan 4, 2023

• multispecies-domain-adaptation

  Public
  Python

  •00 forks in seqcode/multispecies-domain-adaptation•00 stars in seqcode/multispecies-domain-adaptation•00 issues in seqcode/multispecies-domain-adaptation•00 pull requests in seqcode/multispecies-domain-adaptation•Updated Oct 6, 2022Oct 6, 2022

• cross-species-domain-adaptation

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

  transcription-factorsdeep-learninggenomics+ 2

  transcription-factorsdeep-learninggenomicscomparative-genomicsdomain-adaptation

  Jupyter Notebook

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  MIT License

  •55 forks in seqcode/cross-species-domain-adaptation•1212 stars in seqcode/cross-species-domain-adaptation•11 issue in seqcode/cross-species-domain-adaptation•00 pull requests in seqcode/cross-species-domain-adaptation•Updated Aug 29, 2022Aug 29, 2022

• sequnwinder

  Public
  SeqUnwinder: a platform for deconvolving motifs associated with genomic labels

  Java

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  MIT License

  •00 forks in seqcode/sequnwinder•88 stars in seqcode/sequnwinder•22 issues in seqcode/sequnwinder•00 pull requests in seqcode/sequnwinder•Updated Aug 29, 2022Aug 29, 2022

• multigps

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

  Java

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  MIT License

  •22 forks in seqcode/multigps•33 stars in seqcode/multigps•22 issues in seqcode/multigps•00 pull requests in seqcode/multigps•Updated Aug 29, 2022Aug 29, 2022

• multimds

  Public
  Python

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  MIT License

  •00 forks in seqcode/multimds•11 star in seqcode/multimds•11 issue in seqcode/multimds•00 pull requests in seqcode/multimds•Updated Jun 29, 2022Jun 29, 2022

• pegr-docker

  Public
  Dockerfile

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  MIT License

  •00 forks in seqcode/pegr-docker•00 stars in seqcode/pegr-docker•00 issues in seqcode/pegr-docker•00 pull requests in seqcode/pegr-docker•Updated Mar 30, 2022Mar 30, 2022

• cegr-galaxy

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

  Python

  •22 forks in seqcode/cegr-galaxy•33 stars in seqcode/cegr-galaxy•11 issue in seqcode/cegr-galaxy•00 pull requests in seqcode/cegr-galaxy•Updated Dec 1, 2021Dec 1, 2021

• domain_adaptive_nn

  Public
  Cross-species TF binding prediction

  Jupyter Notebook

  •11 fork in seqcode/domain_adaptive_nn•00 stars in seqcode/domain_adaptive_nn•00 issues in seqcode/domain_adaptive_nn•00 pull requests in seqcode/domain_adaptive_nn•Updated Oct 17, 2021Oct 17, 2021