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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 11

  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 5 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 2

Repositories

Showing 10 of 57 repositories
  • 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 4 0 Updated Dec 30, 2025
  • leafworker Public

    An awesome snakemake pipeline to run leafcutter and IsoformSwitchAnalyzeR.

    OpenOmics/leafworker’s past year of commit activity
    Python 1 MIT 0 3 0 Updated Dec 30, 2025
  • 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 Dec 19, 2025
  • fragmentomics Public

    A pipeline analyzing fragmentomics profile of cfDNA sequencing data

    OpenOmics/fragmentomics’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Dec 19, 2025
  • NHLBI-1084 Public

    NHLBI-1084

    OpenOmics/NHLBI-1084’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Dec 16, 2025
  • dockerfiles Public

    Dockerfiles for reproducible scientific research and beyond!

    OpenOmics/dockerfiles’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Dec 15, 2025
  • 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 2 5 0 Updated Dec 15, 2025
  • mir-seek Public

    An awesome microRNA-sequencing pipeline

    OpenOmics/mir-seek’s past year of commit activity
    Python 2 MIT 1 2 0 Updated Dec 15, 2025
  • 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 11 0 0 Updated Dec 12, 2025
  • scribble Public

    Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners

    OpenOmics/scribble’s past year of commit activity
    Python 4 MIT 4 0 0 Updated Dec 5, 2025
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