mobileRNA
This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see mobileRNA.
mobileRNA: Investigate the RNA mobilome & population-scale changes
Bioconductor version: 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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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) (1 year) |
| 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 |
See More
| 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_1.2.0.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 |