SpatialPip: Run a post-quantification 10X technology-format Spatial...

In eudoraleer/Ursa: An Automated Multi-omics Package for Single-cell Analysis

Run a post-quantification 10X technology-format Spatial Transcriptomics pipeline

Description

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

Usage

SpatialPip(
  project_name = "Ursa_Spatial",
  input_dir = "./",
  output_dir = "./",
  pheno_file,
  rnaseq_dir = "./",
  run_rnaseq = FALSE
)

Arguments

project_name	Project name. 'Ursa_Spatial' 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.
rnaseq_dir	scRNA-seq data files directory. We recommend putting the scRNA-seq data in a separate directory separating them from spatial input files. scRNA-seq files should be filtered .h5 format files from 10X Genomics and their file names should have the same sample ID as file prefix to their correspond spatial files.
run_rnaseq	If scRNA-seq integration with spatial data should be run. Default to FALSE. There is no need to prepare scRNA-seq folder if run_rnaseq is set to FALSE.

eudoraleer/Ursa documentation built on Nov. 26, 2022, 10:35 p.m.