DESCRIPTION

Package: mobileRNA
Type: Package
Title: mobileRNA: Investigate the RNA mobilome & population-scale changes
Version: 1.0.15
Authors@R: c(person("Katie", "Jeynes-Cupper", 
    email = "kejc@illinois.edu", role = c("aut", "cre"), 
     comment = c(ORCID = "0009-0000-1350-1371")),
    person("Marco", "Catoni", email = "m.catoni@bham.ac.uk", role = "aut", 
    comment= c(ORCID = "0000-0002-3258-2522")))
Description: 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. 
License: MIT + file LICENSE
Depends:
    R (>= 4.3.0)
VignetteBuilder:
    knitr
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle
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
biocViews: 
    Visualization,
    RNASeq,
    Sequencing,
    SmallRNA,
    GenomeAssembly,
    Clustering,
    ExperimentalDesign,
    QualityControl,
    WorkflowStep, 
    Alignment, 
    Preprocessing
BiocType: Software
BugReports: https://github.com/KJeynesCupper/mobileRNA/issues
SystemRequirements: 
    GNU make, 
    ShortStack (>= 4.0),
    HTSeq,
    HISAT2,
    SAMtools,
    Conda