vignette("scdrake_docker")
)vignette("scdrake")
vignette("scdrake_integration")
vignette("scdrake_advanced")
vignette("scdrake_extend")
{drake}
basics: vignette("drake_basics")
{drake}
book: https://books.ropensci.org/drake/vignette("pipeline_overview")
vignette("scdrake_faq")
vignette("scdrake_cli")
vignette("scdrake_config")
vignette("scdrake_envvars")
vignette("config_pipeline")
vignette("config_main")
01_input_qc
: reading in data, filtering, quality control -> vignette("stage_input_qc")
02_norm_clustering
: normalization, HVG selection, dimensionality reduction, clustering, cell type annotation
-> vignette("stage_norm_clustering")
01_integration
: reading in data and integration -> vignette("stage_integration")
02_int_clustering
: post-integration clustering and cell annotation -> vignette("stage_int_clustering")
cluster_markers
-> vignette("stage_cluster_markers")
contrasts
(differential expression) -> vignette("stage_contrasts")
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