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    54 repositories

    • MPRA-MNIST

      Public
      MPRA-MNIST datasets
      Jupyter Notebook
      •1•18•0•0•Updated Sep 4, 2026Sep 4, 2026

    • EPIC_scoring

      Public
      Public scoring system for EPIC competition submissions
      Python
      •0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • opera_webface

      Public
      Webface for OperaHouse (included inside)
      Ruby
      •
      MIT License
      •0•0•0•2•Updated Sep 3, 2026Sep 3, 2026

    • epifactors_webapp

      Public
      Web-site for EpiFactors database of epigenetic factors, corresponding genes and products.
      websiteepigenetics
      websiteepigenetics
      Ruby
      •1•0•0•2•Updated Sep 3, 2026Sep 3, 2026

    • hocomoco_webapp

      Public
      Web-site for HOCOMOCO collection of transcription factor binding sites motifs.
      websitemotifstfbs
      websitemotifstfbs
      Ruby
      •0•0•0•1•Updated Sep 3, 2026Sep 3, 2026

    • MARADONER

      Public
      Motif Response Analysis Done Right
      Python
      •0•2•0•0•Updated Aug 19, 2026Aug 19, 2026

    • ebin

      Public
      Normalization of MPRA data (FACS bins × replicates × sequences)
      Python
      •0•0•0•0•Updated Aug 13, 2026Aug 13, 2026

    • BABACHI

      Public
      Python
      •
      Other
      •0•3•1•0•Updated Jul 29, 2026Jul 29, 2026

    • GAME-LegNet-predictor-CAGI5-evaluator

      Public
      This repository contains code written by Nikita Penzin for the MPRALegNet predictor and CAGI5 (Kircher) evaluator for the GAME project.
      Python
      •0•0•0•0•Updated Jul 17, 2026Jul 17, 2026

    • MixALime

      Public
      Mixture Models for Allelic Imbalance Estimation
      geneticsasvallele-specific
      geneticsasvallele-specificallele-specific-expressionallelic-imbalance
      Python
      •1•11•0•0•Updated Jul 6, 2026Jul 6, 2026

    • parade

      Public
      Jupyter Notebook
      •
      MIT License
      •4•6•1•0•Updated May 20, 2026May 20, 2026

    • ArChIPelago

      Public
      ArChIPelago — the arrangement of multiple position weight matrices with ChIP-Seq and machine learning for prediction of transcription factor binding sites
      Roff
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • perspectives-on-codebook-allele-specificity

      Public
      "Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors" — allele specificity analysis
      Jupyter Notebook
      •0•1•0•0•Updated Apr 4, 2026Apr 4, 2026

    • ArChIPelago-TFBS-finder

      Public
      Python
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • fantomus-clustering

      Public
      FANTOMUS: Pipeline for clustering CAGE-seq bigWig files into promoters and enhancers using cagefightr
      R
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • ibis-challenge

      Public
      Repository with source code and metadata for IBIS challenge
      Python
      •1•3•0•0•Updated Jan 20, 2026Jan 20, 2026

    • sequence_logo

      Public
      SequenceLogo is a tool for drawing sequence logos of motifs
      Ruby
      •
      MIT License
      •1•1•0•1•Updated Jan 15, 2026Jan 15, 2026

    • maradoner-benchmark

      Public
      MARADONER: Simulation studies
      Raku
      •0•0•0•0•Updated Jan 10, 2026Jan 10, 2026

    • hocomoco_v9

      Public
      Old version of HOCOMOCO TFBS motif database, version 9: https://autosome.ru/HOCOMOCO
      HTML
      •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • postibis

      Public
      IBIS post-challenge models training and testing
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • IBIS-rSNP

      Public
      IBIS rSNP benchmarking
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • sarus

      Public
      SPRY-SARUS motif scanner
      Java
      •0•4•1•0•Updated Jul 23, 2025Jul 23, 2025

    • LegNet

      Public
      accurate prediction of promoter activity and variant effects from massive parallel reporter assays
      Jupyter Notebook
      •
      MIT License
      •3•44•0•0•Updated Jul 3, 2025Jul 3, 2025

    • greco-bit-data-processing

      Public
      Ruby
      •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • TSV_data_for_Codebook_MEX_figures

      Public
      0•0•0•0•Updated Jun 15, 2025Jun 15, 2025

    • MEX-ArChIPelago

      Public
      This repository allows reproducing the MEX-ArChIPelago analysis
      Jupyter Notebook
      •0•0•0•0•Updated May 30, 2025May 30, 2025

    • ASB-frontend

      Public
      TypeScript
      •1•0•0•0•Updated Apr 22, 2025Apr 22, 2025

    • ASB-backend

      Public
      Python
      •1•0•0•8•Updated Apr 13, 2025Apr 13, 2025

    • ArmNet

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated 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
      •3•1•0•1•Updated Dec 30, 2024Dec 30, 2024
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