scRNA_quan: scRNA expression quantification with Salmon.

In sunshanwen/BP4RNAseq: A babysitter's package for reproducible RNA-seq analysis

scRNA expression quantification with Salmon.

Description

scRNA expression quantification with Salmon.

Usage

scRNA_quan(
  transcript,
  protocol,
  threads = 4,
  salmon_index_add = NULL,
  salmon_alevin_add = NULL
)

Arguments

transcript	the reference transcript
protocol	the single-cell RNA sequencing protocol: dropseq, chromium, or chromiumV3.
threads	the number of threads to be used. Default is 4.
salmon_index_add	additional parameters to customize salmon index command. Default is NULL.
salmon_alevin_add	additional parameters to customize salmon alevin command. Default is NULL.

Value

None

Examples

scRNA_quan(transcript = 'test_transcript_Homo_sapiens.fna', protocol = 'dropseq')

sunshanwen/BP4RNAseq documentation built on March 28, 2022, 5:35 p.m.