Run standardized Seurat pipeline

Source: R/seurat_pipeline.R

Run Seurat pipeline on Seurat object or raw counts and meta.data.

seurat_pipeline(
  seurat_obj = NULL,
  counts = NULL,
  meta.data = NULL,
  nfeatures = 2000,
  vars.to.regress = NULL,
  dims = 1:50,
  add_specificity = F,
  assay_name = "RNA",
  default_assay = NULL,
  n.components = 2L,
  log_norm = F,
  parallelize = T,
  seed = 2020
)

Details

Automatically performs

FindVariableFeatures

Variable feature selection

NormalizeData

Data normalization

RunPCA

PCA

RunUMAP

UMAP

FindNeighbors

K-nearest neighbors

FindClusters

Clustering