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@bcbio

Blue Collar Bioinformatics

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Hi there 👋

🙋‍♀️ Welcome!

This project started in the Harvard Chan Bioinformatics Core as a framework to analyze sequencing data. We have migrated the vision to contain templates for downstream analysis of nf-core pipelines

Check committee meetings notes 📝

👩‍💻 Useful resources

Here we list all the reports we mantain currently:

🌈 Contribution guidelines

Thank you for considering contributing to our project! We welcome contributions that enhance the functionality, usability, and reliability of this repository, dedicated to providing template reports for performing downstream analysis of genomic data.

How Can You Contribute?

  1. Go to the report specific repostiory
  2. Report an Issue: If you encounter bugs, have a feature request, or see opportunities for improvement, please open a draftissue in the project board, or an issue in the specific report repository listed above.
  3. Improve Documentation: Contributions to improve documentation, such as correcting typos or adding examples and explanations, are always welcome.
  4. Code Contributions: If you want to contribute code, please read the guidelines below to ensure your contribution can be smoothly integrated.

🍿 Fun facts

Too many to list here!

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  1. bcbioR Public

    R package with well defined templates for most common pipelines

    R 9 3

  2. rnaseq-reports Public template

    code templates and training materials to perform downs-tream analysis from nf-core RNAseq pipelines

    R 2 1

  3. bcbioR-test-data Public

    repository to host small dataset for bcbioR package

    R

  4. singlecell-reports Public template

    code templates and training materials to perform downstream analysis from scRNA preprocessing

    R 1

Repositories

Showing 10 of 26 repositories
  • .github Public
    0 0 0 0 Updated Apr 22, 2025
  • rnaseq-reports Public template

    code templates and training materials to perform downs-tream analysis from nf-core RNAseq pipelines

    R 2 1 1 2 Updated Apr 22, 2025
  • singlecell-reports Public template

    code templates and training materials to perform downstream analysis from scRNA preprocessing

    R 1 0 2 0 Updated Apr 17, 2025
  • bcbioR-test-data Public

    repository to host small dataset for bcbioR package

    R 0 MIT 0 0 0 Updated Apr 15, 2025
  • bcbioR Public

    R package with well defined templates for most common pipelines

    R 9 3 28 0 Updated Apr 4, 2025
  • nextflow-subsample Public

    subsampling fastq files for downstream samples

    Nextflow 0 MIT 0 1 0 Updated Dec 20, 2024
  • resources Public

    files used regularly in downstream analysis of NGS data

    0 MIT 1 0 0 Updated Oct 2, 2024
  • smrnaseq Public Forked from nf-core/smrnaseq

    A small-RNA sequencing analysis pipeline

    Nextflow 0 MIT 127 0 1 Updated Sep 4, 2024
  • bcbio-nextgen Public

    Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

    Python 1,004 MIT 353 129 3 Updated Aug 24, 2024
  • bcbio.github.io Public

    Blue Collar Bioinformatics website

    HTML 9 3 0 0 Updated Apr 30, 2024