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@OpenOmics

OpenOmics

Open Bioinformatics Research
README.md

Welcome to OpenOmics

GIF

We are a diverse group of Bioinformatics scientists, developers, and data scientists on a mission to push science forward.

We believe in open, reproducible, collaborative scientific research, and the strength of community led efforts. We recognize that together as a group we build strong. OpenOmics serves as a place to connect and engage with other community members, share ideas, and build pipelines & tools that enable the greater scientific community.

If you are a new member, welcome! Before getting started, please take a moment to read through our code of conduct. If you have any questions, please feel free to start a discussion.

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  1. genome-seek genome-seek Public

    Clinical Whole Genome and Exome Sequencing Pipeline

    Python 29 12

  2. RNA-seek RNA-seek Public

    Forked from skchronicles/RNA-seek

    A comprehensive quality-control and quantification RNA-seq pipeline

    Python 5 3

  3. modr modr Public

    An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

    Python 6 1

  4. metavirs metavirs Public

    Viral Metagenomics Assembly and Annotation Pipeline

    Python 6 1

  5. cell-seek cell-seek Public

    One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

    Python 2 1

  6. chrom-seek chrom-seek Public

    An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

    Python 5 3

Repositories

Showing 10 of 60 repositories
  • NCBR-533 Public

    Identifying antibiotic resistance genes in all publicly available Staphylococcus aureus genomic and plasmid sequences

    OpenOmics/NCBR-533’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 29, 2026
  • openomics.github.io Public

    OpenOmics home page

    OpenOmics/openomics.github.io’s past year of commit activity
    Python 0 0 3 0 Updated Jan 29, 2026
  • cell-seek Public

    One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

    OpenOmics/cell-seek’s past year of commit activity
    Python 2 MIT 1 5 0 Updated Jan 28, 2026
  • ShinyCell2 Public Forked from the-ouyang-lab/ShinyCell2

    ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data with customizable, publication-ready visualizations.

    OpenOmics/ShinyCell2’s past year of commit activity
    R 0 GPL-3.0 12 0 0 Updated Jan 26, 2026
  • leafworker Public

    An awesome alternative-splicing pipeline that runs leafcutter and IsoformSwitchAnalyzeR.

    OpenOmics/leafworker’s past year of commit activity
    Python 1 MIT 0 3 0 Updated Jan 22, 2026
  • RNA-seek Public Forked from skchronicles/RNA-seek

    A comprehensive quality-control and quantification RNA-seq pipeline

    OpenOmics/RNA-seek’s past year of commit activity
    Python 5 MIT 13 0 0 Updated Jan 21, 2026
  • shiny-forge Public

    A tool to deploy shinycell applications to infinity and beyond (dockerhub and GCP)!

    OpenOmics/shiny-forge’s past year of commit activity
    Python 0 MIT 0 3 0 Updated Jan 20, 2026
  • chrom-seek Public

    An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

    OpenOmics/chrom-seek’s past year of commit activity
    Python 5 MIT 3 7 1 Updated Jan 16, 2026
  • iso-seek Public

    An awesome pipeline for processing bulk PacBio transcriptomics data generated with ISO-seq and MAS-seq.

    OpenOmics/iso-seek’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 16, 2026
  • snakevision Public

    An awesome tool to visualize snakemake rule graphs

    OpenOmics/snakevision’s past year of commit activity
    Python 15 MIT 0 1 0 Updated Jan 9, 2026
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