DOI: 10.18129/B9.bioc.BP4RNAseq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BP4RNAseq.

A babysitter's package for reproducible RNA-seq analysis

Bioconductor version: 3.16

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 gmail.com>

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


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HTML R Script BP4RNAseq vignette


biocViews GeneExpressionWorkflow, Workflow
Version 1.8.0
License GPL-2
Depends R (>= 4.0.0)
Imports dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr, reticulate
Suggests knitr, rmarkdown, testthat
SystemRequirements 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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Source Package BP4RNAseq_1.8.0.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/BP4RNAseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BP4RNAseq
Package Short Url https://bioconductor.org/packages/BP4RNAseq/
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