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@bcbio

Blue Collar Bioinformatics

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

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

👩‍💻 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 bcbioR Public

    R package with well defined templates for most common pipelines

    R 8 3

  2. rnaseq-reports rnaseq-reports Public template

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

    R 1 1

  3. bcbioR-test-data bcbioR-test-data Public

    repository to host small dataset for bcbioR package

    R

  4. singlecell-reports singlecell-reports Public template

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

    R

Repositories

Showing 10 of 26 repositories
  • rnaseq-reports Public template

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

    bcbio/rnaseq-reports’s past year of commit activity
    R 1 1 1 2 Updated Apr 5, 2025
  • bcbioR Public

    R package with well defined templates for most common pipelines

    bcbio/bcbioR’s past year of commit activity
    R 8 3 28 0 Updated Apr 4, 2025
  • singlecell-reports Public template

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

    bcbio/singlecell-reports’s past year of commit activity
    R 0 0 3 0 Updated Apr 4, 2025
  • .github Public
    bcbio/.github’s past year of commit activity
    0 0 0 0 Updated Apr 3, 2025
  • bcbioR-test-data Public

    repository to host small dataset for bcbioR package

    bcbio/bcbioR-test-data’s past year of commit activity
    R 0 MIT 0 0 0 Updated Feb 17, 2025
  • nextflow-subsample Public

    subsampling fastq files for downstream samples

    bcbio/nextflow-subsample’s past year of commit activity
    Nextflow 0 MIT 0 1 0 Updated Dec 20, 2024
  • resources Public

    files used regularly in downstream analysis of NGS data

    bcbio/resources’s past year of commit activity
    0 MIT 1 0 0 Updated Oct 2, 2024
  • smrnaseq Public Forked from nf-core/smrnaseq

    A small-RNA sequencing analysis pipeline

    bcbio/smrnaseq’s past year of commit activity
    Nextflow 0 MIT 128 0 1 Updated Sep 4, 2024
  • bcbio-nextgen Public

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

    bcbio/bcbio-nextgen’s past year of commit activity
    Python 1,002 MIT 354 129 3 Updated Aug 24, 2024
  • bcbio.github.io Public

    Blue Collar Bioinformatics website

    bcbio/bcbio.github.io’s past year of commit activity
    HTML 9 3 0 0 Updated Apr 30, 2024
View all repositories

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