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A babysitter's package for reproducible RNA-seq analysis

Bioconductor version: Release (3.19)

An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. The package can process bulk RNA-seq data and single-cell RNA-seq data. You can only provide the taxa name and the accession id of RNA-seq data deposited in the National Center for Biotechnology Information (NCBI). After a cup of tea or longer, you will get formated gene expression data as gene count and transcript count based on both alignment-based and alignment-free workflows.

Author: Shanwen Sun [cre, aut], Lei Xu [aut], Quan Zou [aut]

Maintainer: Shanwen Sun <sunshanwen at>

Citation (from within R, enter citation("BP4RNAseq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

BP4RNAseq vignette HTML R Script


biocViews GeneExpressionWorkflow, Workflow
Version 1.14.0
License GPL-2
Depends R (>= 4.0.0)
Imports dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr, reticulate
System Requirements UNIX, SRA Toolkit=2.10.3, Entrez Direct=13.3, FastQC=v0.11.9, Cutadapt=2.10, datasets, SAMtools=1.9, HISAT2=2.2.0, StringTie=2.1.1, Salmon=1.2.1
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BP4RNAseq_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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