DESCRIPTION

Package: FLAMES
Title: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Version: 2.1.6
Date: 2023-03-27
Authors@R: c(
       person("Luyi", "Tian", role=c("aut"),
              email="tian.l@wehi.edu.au"),
       person("Changqing", "Wang", role=c("aut", "cre"),
              email="wang.ch@wehi.edu.au"),
       person("Yupei", "You", role=c("aut"),
              email="you.yu@wehi.edu.au"),
       person("Oliver", "Voogd", role=c("aut"),
              email="voogd.o@wehi.edu.au"),
       person("Jakob", "Schuster", role=c("aut"),
              email="schuster.j@wehi.edu.au"),
       person("Shian",  "Su", role=c("aut"),
              email="su.s@wehi.edu.au"),
       person("Matthew", "Ritchie",role=c("ctb"),
              email="mritchie@wehi.edu.au"))
Description: Semi-supervised isoform detection and annotation from both bulk and single-cell 
  long read RNA-seq data. Flames provides automated pipelines for analysing isoforms,
  as well as intermediate functions for manual execution.
biocViews: RNASeq, SingleCell, Transcriptomics, DataImport, 
            DifferentialSplicing, AlternativeSplicing, GeneExpression,
            LongRead
BugReports: https://github.com/mritchielab/FLAMES/issues
License: GPL (>= 3)
Encoding: UTF-8
Imports: 
    basilisk,
    bambu,
    BiocParallel,
    Biostrings,
    BiocGenerics,
    circlize,
    ComplexHeatmap,
    cowplot,
    dplyr,
    DropletUtils,
    GenomicRanges,
    GenomicFeatures,
    txdbmaker,
    GenomicAlignments,
    GenomeInfoDb,
    ggplot2,
    ggbio,
    grid,
    gridExtra,
    igraph,
    jsonlite,
    magrittr,
    magick,
    Matrix,
    MatrixGenerics,
    readr,
    reticulate,
    Rsamtools,
    rtracklayer,
    RColorBrewer,
    SingleCellExperiment,
    SummarizedExperiment,
    SpatialExperiment,
    scater,
    scatterpie,
    S4Vectors,
    scuttle,
    stats,
    scran,
    stringr,
    tidyr,
    utils,
    withr,
    future,
    methods,
    tibble,
    tidyselect,
    IRanges
Suggests:
    BiocStyle,
    GEOquery,
    knitr,
    rmarkdown,
    BiocFileCache,
    R.utils,
    ShortRead,
    uwot,
    testthat (>= 3.0.0),
    xml2
LinkingTo: Rcpp, Rhtslib, testthat
SystemRequirements: GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://mritchielab.github.io/FLAMES
Config/testthat/edition: 3
Depends: 
    R (>= 4.1.0)
LazyData: true
LazyLoad: yes
StagedInstall: no