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
| Maintainer | Katie Jeynes-Cupper <kejc@illinois.edu> |
| Author | Katie Jeynes-Cupper [aut, cre] (ORCID: <https://orcid.org/0009-0000-1350-1371>), Marco Catoni [aut] (ORCID: <https://orcid.org/0000-0002-3258-2522>) |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/KJeynesCupper/mobileRNA/issues |
| System Requirements | GNU make, ShortStack (>= 4.0), HTSeq, HISAT2, SAMtools, Conda |
| Downloads rank | 199 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Clustering, ExperimentalDesign, GenomeAssembly, Preprocessing, QualityControl, RNASeq, Sequencing, SmallRNA, Software, Visualization, WorkflowStep |
Documentation
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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)