Package: FLAMES
Title: FLAMES: Full Length Analysis of Mutations and Splicing in long
        read RNA-seq data
Version: 2.7.0
Date: 2025-07-22
Authors@R: c(
       person("Changqing", "Wang", role=c("aut", "cre"),
              email="wang.ch@wehi.edu.au"),
       person("Luyi", "Tian", role=c("aut"),
              email="tian.l@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("Yair D.J.", "Prawer", role=c("aut"),
              email="sefi.prawer@unimelb.edu.au"),
       person("Yupei", "You", role=c("aut"),
              email="you.yu@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: abind, basilisk, bambu, BiocParallel, Biostrings,
        BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli,
        dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments,
        Seqinfo, ggplot2, grid, gridExtra, igraph, jsonlite, magrittr,
        magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools,
        rtracklayer, RColorBrewer, R.utils, S4Arrays, ShortRead,
        SingleCellExperiment, SummarizedExperiment, SpatialExperiment,
        scater, scatterpie, scrapper (>= 1.5.17), S4Vectors, scuttle,
        stats, scran, stringr, tidyr, utils, withr, methods, tibble,
        tidyselect, IRanges
Suggests: BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot,
        testthat (>= 3.0.0), xml2
LinkingTo: Rcpp, Rhtslib, testthat
SystemRequirements: GNU make, C++17
Config/Bioconductor/UnsupportedPlatforms: windows
RoxygenNote: 7.3.3
VignetteBuilder: knitr
URL: https://mritchielab.github.io/FLAMES
Config/testthat/edition: 3
Depends: R (>= 4.2.0)
LazyLoad: yes
StagedInstall: no
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev perl python3 libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-05 08:58:49 UTC
RemoteUrl: https://github.com/bioc/FLAMES
RemoteRef: HEAD
RemoteSha: 38fd4e3299f60f858d1cc74845c8c12c5c23a164
NeedsCompilation: yes
Packaged: 2026-07-05 10:13:29 UTC; root
Author: Changqing Wang [aut, cre],
  Luyi Tian [aut],
  Oliver Voogd [aut],
  Jakob Schuster [aut],
  Shian Su [aut],
  Yair D.J. Prawer [aut],
  Yupei You [aut],
  Matthew Ritchie [ctb]
Maintainer: Changqing Wang <wang.ch@wehi.edu.au>