BP4RNAseq
A babysitter's package for reproducible RNA-seq analysis
Bioconductor version: 3.23 · Package version: 1.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BP4RNAseq")Details
| Maintainer | Shanwen Sun <sunshanwen@gmail.com> |
| Author | Shanwen Sun [cre, aut], Lei Xu [aut], Quan Zou [aut] |
| License | GPL-2 |
| 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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpressionWorkflow, Workflow |
| Package Short Url | https://bioconductor.org/packages/BP4RNAseq/ |
Citation
From within R, enter 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.
Download
Follow the installation instructions to use this package in your R session.
| Source package | BP4RNAseq_1.22.0.tar.gz |