mobileRNA

mobileRNA: Investigate the RNA mobilome & population-scale changes

Bioconductor version: Release (3.20)

Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.

Author: Katie Jeynes-Cupper [aut, cre] , Marco Catoni [aut]

Maintainer: Katie Jeynes-Cupper <kej031 at student.bham.ac.uk>

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

Installation

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


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

BiocManager::install("mobileRNA")

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("mobileRNA")

mobileRNA	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Clustering, ExperimentalDesign, GenomeAssembly, Preprocessing, QualityControl, RNASeq, Sequencing, SmallRNA, Software, Visualization, WorkflowStep
Version	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid
System Requirements	GNU make, ShortStack (>= 4.0), HTSeq, HISAT2, SAMtools, Conda
URL
Bug Reports	https://github.com/KJeynesCupper/mobileRNA/issues

Suggests	knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	mobileRNA_1.2.0.tar.gz
Windows Binary (x86_64)	mobileRNA_1.2.0.zip
macOS Binary (x86_64)	mobileRNA_1.2.0.tgz
macOS Binary (arm64)	mobileRNA_1.1.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mobileRNA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mobileRNA
Bioc Package Browser	https://code.bioconductor.org/browse/mobileRNA/
Package Short Url	https://bioconductor.org/packages/mobileRNA/
Package Downloads Report	Download Stats