bcbio-nextgen
stable
  • Getting started

User stories

  • Somatic (cancer) variants
  • Bulk RNA-seq
  • Counting cells and transcripts for inDrops3 data
  • PureCN analysis of tumor-only samples
  • HLA typing
  • Small germline variants
  • 3’ DGE
  • Structural variant calling
  • ATAC-seq
  • Methylation
  • Variant calling using bulk RNA-seq data
  • Detecting gene fusions with bulk RNA-seq data
  • fast RNA-seq
  • Disambiguation
  • smallRNA-seq

Infrastructure

  • Installation
  • Configuration
  • Parallel execution
  • Outputs
  • Common Workflow Language (CWL)
  • Cloud
  • Development

Misc

  • Users
  • Internals
  • Presentations
  • Teaching
  • Single cell RNA-seq analysis
  • Cancer tumor-normal variant calling
  • Citations
bcbio-nextgen
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