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@bcbio Blue Collar Bioinformatics

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    22 repositories

    • bcbioR

      Public
      R package with well defined templates for most common pipelines
      R
      •
      Other
      •1•3•23•1•Updated Nov 14, 2024Nov 14, 2024

    • bcbioR-test-data

      Public
      repository to host small dataset for bcbioR package
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • resources

      Public
      files used regularly in downstream analysis of NGS data
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •125•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
      •354•994•131•3•Updated Aug 24, 2024Aug 24, 2024

    • bcbio.github.io

      Public
      Blue Collar Bioinformatics website
      HTML
      •3•9•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
      •12•20•0•0•Updated Nov 3, 2021Nov 3, 2021

    • bcbio_docker

      Public
      Automated Docker builds for bcbio
      Dockerfile
      •
      MIT License
      •4•7•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
      •12•0•0•0•Updated Oct 28, 2020Oct 28, 2020

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.3k•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
      •158•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•65•22•0•Updated Jun 3, 2020Jun 3, 2020

    • bcbio.variation.recall

      Public
      Parallel merging, squaring off and ensemble calling for genomic variants
      Clojure
      •3•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