Skip to content

@bcbio Blue Collar Bioinformatics

Change the repository type filter

All

    Repositories list

    29 repositories

    • resources

      Public
      files used regularly in downstream analysis of NGS data
      MIT License
      •2•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • rnaseq-reports

      Public template
      code templates and training materials to perform downs-tream analysis from nf-core RNAseq pipelines
      R
      •5•15•6•6•Updated Dec 5, 2025Dec 5, 2025

    • singlecell-reports

      Public template
      code templates and training materials to perform downstream analysis from scRNA preprocessing
      R
      •2•6•5•5•Updated Nov 12, 2025Nov 12, 2025

    • peakseq-reports

      Public template
      Analyses for ChIPseq, ATACseq and CutandRun assays
      R
      •0•0•1•3•Updated Oct 8, 2025Oct 8, 2025

    • bcbioR-test-data

      Public
      repository to host small dataset for bcbioR package
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • bcbioR

      Public
      R package with well defined templates for most common pipelines
      R
      •
      Other
      •4•17•27•0•Updated Jul 11, 2025Jul 11, 2025

    • spatial-reports

      Public template
      Reports in markdown, quarto and notebooks to work with spatial single cell from multiple platforms and with multiple packages
      R
      •2•3•0•1•Updated Jul 2, 2025Jul 2, 2025

    • proteomics-reports

      Public template
      Analyses for Olink data
      R
      •1•0•1•1•Updated May 29, 2025May 29, 2025

    • .github

      Public
      0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • nextflow-subsample

      Public
      subsampling fastq files for downstream samples
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Dec 20, 2024Dec 20, 2024

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •133•0•0•1•Updated Sep 4, 2024Sep 4, 2024

    • bcbio-nextgen

      Public
      Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
      Python
      •
      MIT License
      •355•1k•129•3•Updated Aug 24, 2024Aug 24, 2024

    • bcbio.github.io

      Public
      Blue Collar Bioinformatics website
      HTML
      •3•10•0•0•Updated Apr 30, 2024Apr 30, 2024

    • hivdrm

      Public
      Detect HIV Drug Resitant Mutations using amplicon sequencing data
      Python
      •
      MIT License
      •1•1•0•0•Updated May 20, 2023May 20, 2023

    • bcbio_validations

      Public
      Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
      HTML
      •11•31•0•0•Updated Feb 12, 2022Feb 12, 2022

    • bcbio_validation_workflows

      Public
      A community menagarie of automated variant validations using bcbio and the Common Workflow Language
      Common Workflow Language
      •
      MIT License
      •13•21•0•0•Updated Nov 3, 2021Nov 3, 2021

    • bcbio_docker

      Public
      Automated Docker builds for bcbio
      Dockerfile
      •
      MIT License
      •3•8•2•0•Updated Apr 22, 2021Apr 22, 2021

    • bcbio-utils

      Public
      Helper scripts for bcbio-nextgen
      Python
      •
      MIT License
      •0•3•2•0•Updated Mar 25, 2021Mar 25, 2021

    • scramble

      Public
      R
      •
      Other
      •11•0•0•0•Updated Oct 28, 2020Oct 28, 2020

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.8k•0•0•0•Updated Oct 26, 2020Oct 26, 2020

    • cloudbiolinux

      Public
      CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
      Python
      •
      MIT License
      •155•0•0•0•Updated Oct 9, 2020Oct 9, 2020

    • bcbio-nextgen-vm

      Public
      Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
      Python
      •
      MIT License
      •17•68•22•0•Updated Jun 3, 2020Jun 3, 2020

    • bcbio.variation.recall

      Public
      Parallel merging, squaring off and ensemble calling for genomic variants
      Clojure
      •4•20•10•0•Updated Sep 17, 2019Sep 17, 2019

    • bcbio_rnaseq_output_example

      Public
      example of bcbio RNAseq output to test bcbioRnaseq R package
      R
      •
      MIT License
      •0•1•0•0•Updated Apr 3, 2019Apr 3, 2019

    • test_bcbio_cwl

      Public
      Test workflows, run scripts and data for bcbio Common Workflow Language integration
      Common Workflow Language
      •
      MIT License
      •8•7•2•0•Updated Jan 25, 2019Jan 25, 2019

    • bcbio-validation-checker

      Public
      Compare validation outputs from bcbio against existing truth sets
      Python
      •1•0•0•0•Updated Oct 4, 2018Oct 4, 2018

    • bcbio-dnanexus-wrapper

      Public
      Repository to hold wrapper apps for bcbio CWL on DNAnexus
      Shell
      •1•2•0•0•Updated Sep 9, 2018Sep 9, 2018

    • bcbio_srnaseq_output_example

      Public
      Example of small RNAseq analysis with bcbio
      HTML
      •0•0•0•0•Updated Feb 21, 2018Feb 21, 2018

    • icr142-validation

      Public
      Preparation scripts and bcbio integration for the ICR142 NGS validation series
      Python
      •1•4•0•0•Updated May 8, 2016May 8, 2016