BP4RNAseq

A babysitter's package for reproducible RNA-seq analysis

Bioconductor version: Release (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BP4RNAseq")

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

Documentation

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

browseVignettes("BP4RNAseq")

BP4RNAseq vignette

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R Script

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpressionWorkflow, Workflow
Version	1.16.0
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
URL

Suggests	knitr, rmarkdown, testthat
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Package Archives

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

Source Package	BP4RNAseq_1.16.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats