BP4RNAseq
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BP4RNAseq.
A babysitter's package for reproducible RNA-seq analysis
Bioconductor version: 3.17
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")):
Installation
To install this package, start R (version "4.3") 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 | 1.10.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
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| Depends On Me | |
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Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BP4RNAseq_1.10.0.tar.gz |
| Windows Binary | |
| 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 |