Package: FLAMES
Title: FLAMES: Full Length Analysis of Mutations and Splicing in long
        read RNA-seq data
Version: 2.4.1
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, ggbio, grid, gridExtra, igraph, jsonlite,
        magrittr, magick, Matrix, MatrixGenerics, readr, reticulate,
        Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays,
        ShortRead, SingleCellExperiment, SummarizedExperiment,
        SpatialExperiment, scater, scatterpie, 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
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://mritchielab.github.io/FLAMES
Config/testthat/edition: 3
Depends: R (>= 4.2.0)
LazyLoad: yes
StagedInstall: no
git_url: https://git.bioconductor.org/packages/FLAMES
git_branch: RELEASE_3_22
git_last_commit: 41bbd55
git_last_commit_date: 2025-10-31
Repository: Bioconductor 3.22
Date/Publication: 2025-10-31
NeedsCompilation: yes
Packaged: 2025-10-31 21:10:14 UTC; biocbuild
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>
Built: R 4.5.1; x86_64-apple-darwin20; 2025-11-01 05:34:34 UTC; unix
