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This is the development version of BP4RNAseq; for the stable release version, see BP4RNAseq.

A babysitter's package for reproducible RNA-seq analysis

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.15.0
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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Suggests knitr, rmarkdown, testthat
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Package Archives

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

Source Package BP4RNAseq_1.15.0.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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