mobileRNA
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see mobileRNA.
mobileRNA: Investigate the RNA mobilome & population-scale changes
Bioconductor version: 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 <kejc at illinois.edu>
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 | 1.0.15 |
In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
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_1.0.15.tar.gz |
Windows Binary (x86_64) | mobileRNA_1.0.15.zip |
macOS Binary (x86_64) | mobileRNA_1.0.15.tgz |
macOS Binary (arm64) | mobileRNA_1.0.15.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/mobileRNA |
Source Repository (Developer Access) | git clone [email protected]:packages/mobileRNA |
Bioc Package Browser | https://code.bioconductor.org/browse/mobileRNA/ |
Package Short Url | https://bioconductor.org/packages/mobileRNA/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.19 | Source Archive |