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    • Web-site for HOCOMOCO collection of transcription factor binding sites motifs.
      Ruby
      0002Updated May 4, 2026May 4, 2026
    • parade

      Public
      Jupyter Notebook
      MIT License
      3500Updated May 4, 2026May 4, 2026
    • MPRA-MNIST datasets
      Jupyter Notebook
      1700Updated May 4, 2026May 4, 2026
    • MixALime

      Public
      Mixture Models for Allelic Imbalance Estimation
      Python
      11100Updated Apr 21, 2026Apr 21, 2026
    • Webface for OperaHouse (included inside)
      Ruby
      MIT License
      0000Updated Apr 16, 2026Apr 16, 2026
    • Web-site for EpiFactors database of epigenetic factors, corresponding genes and products.
      Ruby
      1000Updated Apr 16, 2026Apr 16, 2026
    • MARADONER

      Public
      Motif Response Analysis Done Right
      Python
      0000Updated Apr 5, 2026Apr 5, 2026
    • "Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors" — allele specificity analysis
      Jupyter Notebook
      0000Updated Apr 4, 2026Apr 4, 2026
    • ArChIPelago — the arrangement of multiple position weight matrices with ChIP-Seq and machine learning for prediction of transcription factor binding sites
      Jupyter Notebook
      0000Updated Mar 30, 2026Mar 30, 2026
    • Python
      0000Updated Feb 11, 2026Feb 11, 2026
    • FANTOMUS: Pipeline for clustering CAGE-seq bigWig files into promoters and enhancers using cagefightr
      R
      0000Updated Feb 2, 2026Feb 2, 2026
    • Repository with source code and metadata for IBIS challenge
      Python
      1300Updated Jan 20, 2026Jan 20, 2026
    • SequenceLogo is a tool for drawing sequence logos of motifs
      Ruby
      MIT License
      1101Updated Jan 15, 2026Jan 15, 2026
    • MARADONER: Simulation studies
      Raku
      0000Updated Jan 10, 2026Jan 10, 2026
    • BABACHI

      Public
      Python
      Other
      0310Updated Dec 14, 2025Dec 14, 2025
    • Old version of HOCOMOCO TFBS motif database, version 9: https://autosome.ru/HOCOMOCO
      HTML
      0000Updated Nov 19, 2025Nov 19, 2025
    • postibis

      Public
      IBIS post-challenge models training and testing
      Jupyter Notebook
      MIT License
      0000Updated Oct 15, 2025Oct 15, 2025
    • IBIS-rSNP

      Public
      IBIS rSNP benchmarking
      Jupyter Notebook
      0000Updated Aug 28, 2025Aug 28, 2025
    • sarus

      Public
      SPRY-SARUS motif scanner
      Java
      0310Updated Jul 23, 2025Jul 23, 2025
    • LegNet

      Public
      accurate prediction of promoter activity and variant effects from massive parallel reporter assays
      Jupyter Notebook
      MIT License
      44400Updated Jul 3, 2025Jul 3, 2025
    • Ruby
      0000Updated Jun 16, 2025Jun 16, 2025
    • 0000Updated Jun 15, 2025Jun 15, 2025
    • This repository allows reproducing the MEX-ArChIPelago analysis
      Jupyter Notebook
      0000Updated May 30, 2025May 30, 2025
    • TypeScript
      1000Updated Apr 22, 2025Apr 22, 2025
    • Python
      1008Updated Apr 13, 2025Apr 13, 2025
    • ArmNet

      Public
      Python
      MIT License
      0400Updated Jan 11, 2025Jan 11, 2025
    • pasio

      Public
      Pasio is a tool for denoising profiles coming from DNA-sequencing data like ATAC-seq, DNA-seq or ChIP-seq.
      Python
      Other
      3101Updated Dec 30, 2024Dec 30, 2024
    • Reproduction material for numerical tests in the MixALime paper
      Python
      0000Updated Nov 7, 2024Nov 7, 2024
    • Python
      MIT License
      21600Updated Oct 21, 2024Oct 21, 2024
    • Python
      1100Updated Aug 29, 2024Aug 29, 2024
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