scImmunePip: Run a post-quantification 10X technology-format scImmune...
In eudoraleer/Ursa: An Automated Multi-omics Package for Single-cell Analysis

View source: R/Dubhe.R

scImmunePip

R Documentation

Run a post-quantification 10X technology-format scImmune Profiling pipeline

Description

This function will run a bioinformatics analysis of post-quantification scImmune Profiling pipeline. Supports multiple samples analysis.

Usage

scImmunePip(
  project_name = "Ursa_scImmune",
  input_dir = "./",
  output_dir = "./",
  pheno_file,
  integration_method = c("harmony", "seurat"),
  auto_move = T
)

Arguments

`project_name`	Project name. 'Ursa_scImmune' by default.
`input_dir`	Directory to all input files. Current working directory by default.
`output_dir`	Output directory. Current working directory by default. A new folder with the given project name with time stamp as suffix will be created under the specified output directory.
`pheno_file`	Meta data file directory. Accept only .csv/.txt format files.
`integration_method`	Integration method for combining scRNASeq data. Default by harmony.