down2quan: Download the RNA-seq samples from the NCBI and produce the...

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

Download the RNA-seq samples from the NCBI and produce the quantifications of gene expression.

Description

Download the RNA-seq samples from the NCBI and produce the quantifications of gene expression with alignment-based and alignment-free workflows.

Usage

down2quan(
  accession,
  dir = getwd(),
  taxa,
  novel_transcript = FALSE,
  threads = 4,
  scRNA = FALSE,
  protocol
)

Arguments

accession	the bioproject accession code for the RNA-seq samples deposited in the NCBI.
dir	the working directory. Default is the current working directory.
taxa	the scientific or common name of the organism.
novel_transcript	logic, whether identifying novel transcripts is expected or not. Default is FALSE.
threads	the number of threads to be used. Default is 4.
scRNA	logic, whether single-cell RNA-seq is quantified or not. Default is FALSE.
protocol	the single-cell RNA sequencing protocol: dropseq, chromium, or chromiumV3.

Value

None

Examples

down2quan(
accession = 'SRR11427582', dir = getwd(), 
taxa = 'Drosophila melanogaster', novel_transcript = FALSE, scRNA = FALSE
)

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