Blue Collar Bioinformatics
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Pinned Repositories
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
bcbio-nextgen-vm
Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
bcbio-utils
Helper scripts for bcbio-nextgen
bcbio.github.io
Blue Collar Bioinformatics website
bcbio.variation.recall
Parallel merging, squaring off and ensemble calling for genomic variants
bcbio_validation_workflows
A community menagarie of automated variant validations using bcbio and the Common Workflow Language
bcbio_validations
Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
bcbioR
R package with well defined templates for most common pipelines
cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
test_bcbio_cwl
Test workflows, run scripts and data for bcbio Common Workflow Language integration
Blue Collar Bioinformatics's Repositories
bcbio/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
bcbio/bcbio-nextgen-vm
Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
bcbio/bcbio_validations
Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
bcbio/bcbio.variation.recall
Parallel merging, squaring off and ensemble calling for genomic variants
bcbio/bcbio_validation_workflows
A community menagarie of automated variant validations using bcbio and the Common Workflow Language
bcbio/bcbio.github.io
Blue Collar Bioinformatics website
bcbio/bcbio_docker
Automated Docker builds for bcbio
bcbio/test_bcbio_cwl
Test workflows, run scripts and data for bcbio Common Workflow Language integration
bcbio/icr142-validation
Preparation scripts and bcbio integration for the ICR142 NGS validation series
bcbio/bcbio-dnanexus-wrapper
Repository to hold wrapper apps for bcbio CWL on DNAnexus
bcbio/bcbio-utils
Helper scripts for bcbio-nextgen
bcbio/bcbio_rnaseq_output_example
example of bcbio RNAseq output to test bcbioRnaseq R package
bcbio/bcbioR
R package with well defined templates for most common pipelines
bcbio/hivdrm
Detect HIV Drug Resitant Mutations using amplicon sequencing data
bcbio/cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
bcbio/bcbio-validation-checker
Compare validation outputs from bcbio against existing truth sets
bcbio/bcbio_srnaseq_output_example
Example of small RNAseq analysis with bcbio
bcbio/bcbioR-test-data
repository to host small dataset for bcbioR package
bcbio/bioconda-recipes
Conda recipes for the bioconda channel.
bcbio/scramble