In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

• Guides:
• Using the Docker image: https://bioinfocz.github.io/scdrake/articles/scdrake_docker.html (or vignette("scdrake_docker"))
• 01 Quick start (single-sample pipeline): vignette("scdrake")
• 02 Integration pipeline guide: vignette("scdrake_integration")
• Advanced topics: vignette("scdrake_advanced")
• Extending the pipeline: vignette("scdrake_extend")
• {drake} basics: vignette("drake_basics")
  • Or the official {drake} book: https://books.ropensci.org/drake/
• General information:
• Pipeline overview: vignette("pipeline_overview")
• FAQ & Howtos: vignette("scdrake_faq")
• Command line interface (CLI): vignette("scdrake_cli")
• Config files (internals): vignette("scdrake_config")
• Environment variables: vignette("scdrake_envvars")
• General configs:
  • Pipeline config -> vignette("config_pipeline")
  • Main config -> vignette("config_main")
• Pipelines and stages:
• Single-sample pipeline:
  • Stage 01_input_qc: reading in data, filtering, quality control -> vignette("stage_input_qc")
  • Stage 02_norm_clustering: normalization, HVG selection, dimensionality reduction, clustering, cell type annotation -> vignette("stage_norm_clustering")
• Integration pipeline:
  • Stage 01_integration: reading in data and integration -> vignette("stage_integration")
  • Stage 02_int_clustering: post-integration clustering and cell annotation -> vignette("stage_int_clustering")
• Common stages:
  • Stage cluster_markers -> vignette("stage_cluster_markers")
  • Stage contrasts (differential expression) -> vignette("stage_contrasts")

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.