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mobileRNA

This is the development version of mobileRNA; to use it, please install the devel version of Bioconductor.

mobileRNA: Investigate the RNA mobilome & population-scale changes


Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, Clustering, ExperimentalDesign, GenomeAssembly, Preprocessing, QualityControl, RNASeq, Sequencing, SmallRNA, Software, Visualization, WorkflowStep
Version 0.99.23
In Bioconductor since BioC 3.19 (R-4.4)
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
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Suggests knitr, rmarkdown, BiocStyle
Linking To
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Package Archives

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

Source Package mobileRNA_0.99.23.tar.gz
Windows Binary mobileRNA_0.99.23.zip
macOS Binary (x86_64) mobileRNA_0.99.23.tgz
macOS Binary (arm64) mobileRNA_0.99.23.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