scRNA_quan: scRNA expression quantification with Salmon.

View source: R/scRNA_quan.R

scRNA_quanR Documentation

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.