BP4RNAseq
This is the released version of BP4RNAseq; for the devel version, see BP4RNAseq.
A babysitter's package for reproducible RNA-seq analysis
Bioconductor version: Release (3.23)
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("BP4RNAseq")):Shanwen Sun, Lei Xu, Quan Zou. BP4RNAseq: A babysitter's package for reproducible RNA-seq analysis. doi:10.18129/B9.bioc.BP4RNAseq, R package version 1.22.0, https://bioconductor.org/packages/BP4RNAseq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | HTML | R Script |
Details
| biocViews | GeneExpressionWorkflow, Workflow |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BP4RNAseq_1.22.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |