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mobileRNA

mobileRNA: Investigate the RNA mobilome & population-scale changes

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

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

BiocManager::install("mobileRNA")

Details

MaintainerKatie Jeynes-Cupper <kejc@illinois.edu>
AuthorKatie Jeynes-Cupper [aut, cre] (ORCID: <https://orcid.org/0009-0000-1350-1371>), Marco Catoni [aut] (ORCID: <https://orcid.org/0000-0002-3258-2522>)
LicenseMIT + file LICENSE
Bug Reportshttps://github.com/KJeynesCupper/mobileRNA/issues
System RequirementsGNU make, ShortStack (>= 4.0), HTSeq, HISAT2, SAMtools, Conda
Downloads rank199
Source branchRELEASE_3_23
biocViewsAlignment, Clustering, ExperimentalDesign, GenomeAssembly, Preprocessing, QualityControl, RNASeq, Sequencing, SmallRNA, Software, Visualization, WorkflowStep

Documentation

Download

Dependencies

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

Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)