DESCRIPTION

Package: RNAmodR
Type: Package
Title: Detection of post-transcriptional modifications in high throughput sequencing data
Version: 1.17.1
Date: 2024-03-18
Authors@R: c(person("Felix G.M.", 
                    "Ernst", 
                    email = "felix.gm.ernst@outlook.com", 
                    role = c("aut", "cre"),
                    comment = c(ORCID = "0000-0001-5064-0928")),
             person("Denis L.J.", 
                    "Lafontaine", 
                    email = "denis.lafontaine@ulb.ac.be", 
                    role = c("ctb", "fnd")))
Description: RNAmodR provides classes and workflows for loading/aggregation data
    from high througput sequencing aimed at detecting post-transcriptional 
    modifications through analysis of specific patterns. In addition, utilities
    are provided to validate and visualize the results. The RNAmodR package
    provides a core functionality from which specific analysis strategies can
    be easily implemented as a seperate package.
biocViews: 
    Software, Infrastructure, WorkflowStep, Visualization, Sequencing
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Depends:
    R (>= 4.0),
    S4Vectors (>= 0.27.12),
    IRanges (>= 2.23.9),
    GenomicRanges,
    Modstrings
Imports:
    methods,
    stats,
    grDevices, 
    matrixStats,
    BiocGenerics,
    Biostrings (>= 2.57.2),
    BiocParallel,
    txdbmaker,
    GenomicFeatures,
    GenomicAlignments,
    GenomeInfoDb,
    rtracklayer,
    Rsamtools,
    BSgenome,
    RColorBrewer,
    colorRamps,
    ggplot2,
    Gviz (>= 1.31.0),
    reshape2,
    graphics,
    ROCR
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    RNAmodR.Data
VignetteBuilder: knitr
Collate:
    'RNAmodR.R'
    'AllGenerics.R'
    'Gviz-ModifiedSequenceTrack-class.R'
    'settings.R'
    'Modifier-utils.R'
    'SequenceDataFrame-class.R'
    'normalization.R'
    'SequenceData-class.R'
    'SequenceDataSet-class.R'
    'SequenceDataList-class.R'
    'Modifier-class.R'
    'ModifierSet-class.R'
    'Modifier-Inosine-class.R'
    'Modifier-Inosine-viz.R'
    'Modifier-roc.R'
    'Modifier-subset.R'
    'Modifier-viz.R'
    'ModifierSet-comparison.R'
    'ModifierSet-viz.R'
    'RNAmodR-external-functions.R'
    'RNAmodR-summary.R'
    'SequenceData-coverage.R'
    'SequenceData-end-pos.R'
    'SequenceData-normalized-end-pos.R'
    'SequenceData-pileup.R'
    'SequenceData-viz.R'
    'SequenceData-protected-end-pos.R'
    'SequenceData-stats.R'
    'SequenceData-subset.R'
    'SequenceDataList-viz.R'
    'SequenceDataSet-viz.R'
    'utils-bam.R'
    'utils.R'
RoxygenNote: 7.3.1
BugReports: https://github.com/FelixErnst/RNAmodR/issues
URL: https://github.com/FelixErnst/RNAmodR