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@seqcode

seqcode

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

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  1. miniMDS miniMDS Public

    Python 31 9

  2. allo allo Public

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

    Python 25 5

  3. cross-species-domain-adaptation cross-species-domain-adaptation Public

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

    Jupyter Notebook 12 5

  4. Bichrom Bichrom Public

    Interpretable bimodal network for transcription factors binding site prediction

    Python 10 3

  5. sequnwinder sequnwinder Public

    SeqUnwinder: a platform for deconvolving motifs associated with genomic labels

    Java 8

  6. chexmix chexmix Public

    ChExMix: the ChIP-exo mixture model

    Java 7 1

Repositories

Showing 10 of 45 repositories
  • seqaffinity Public
    seqcode/seqaffinity's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Oct 18, 2026
  • pegr Public

    Platform for Eukaryotic Genome Regulation

    seqcode/pegr's past year of commit activity
    Groovy 4 MIT 1 38 (1 issue needs help) 0 Updated Sep 17, 2026
  • stamp Public

    STAMP

    seqcode/stamp's past year of commit activity
    TypeScript 5 3 1 0 Updated Aug 28, 2026
  • TPCAV Public

    Testing with PCA projected Concept Activation Vectors

    seqcode/TPCAV's past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Aug 26, 2026
  • ncems-simplified Public

    Simplified ENCODE processing pipelines for ChIP-seq and ATAC-seq, incorporating Allo

    seqcode/ncems-simplified's past year of commit activity
    Python 0 0 0 0 Updated Aug 10, 2026
  • bioinformatics-educational-react-apps Public

    A collection of educational bioinformatics apps that illustrate bioinformatics algorithms

    seqcode/bioinformatics-educational-react-apps's past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jul 21, 2026
  • 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 7, 2026
  • chexmix Public

    ChExMix: the ChIP-exo mixture model

    seqcode/chexmix's past year of commit activity
    Java 7 MIT 1 4 0 Updated Oct 24, 2025
  • 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 Jul 18, 2025
  • pfal-chrom-states-trackhub Public

    Plasmodium falciparum chromatin state trackhubs for UCSC genome browser

    seqcode/pfal-chrom-states-trackhub's past year of commit activity
    Python 0 MIT 0 0 0 Updated May 23, 2025

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