mobileRNA
This is the development version of mobileRNA; for the stable release version, see mobileRNA.
mobileRNA: Investigate the RNA mobilome & population-scale changes
Bioconductor version: Development (3.23)
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 "4.6") 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
| Reference Manual |
Details
| biocViews | Alignment, Clustering, ExperimentalDesign, GenomeAssembly, Preprocessing, QualityControl, RNASeq, Sequencing, SmallRNA, Software, Visualization, WorkflowStep |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/mobileRNA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mobileRNA |
| Package Short Url | https://bioconductor.org/packages/mobileRNA/ |
| Package Downloads Report | Download Stats |