Package: FLAMES
Type: Package
Title: FLAMES: Full Length Analysis of Mutations and Splicing in long
        read RNA-seq data
Version: 1.8.0
Date: 2023-10-2
Authors@R: c(
       person("Luyi", "Tian", role=c("aut"),
              email="tian.l@wehi.edu.au"),
       person("Changqing", "Wang", role=c("aut"),
              email="wang.ch@wehi.edu.au"),
       person("Youpei", "You", role=c("aut"),
              email="you.yu@wehi.edu.au"),
       person("Oliver", "Voogd", role=c("aut", "cre"),
              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
License: GPL (>= 2)
Encoding: UTF-8
Imports: basilisk, bambu, Biostrings, BiocGenerics, circlize,
        ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges,
        GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2,
        ggbio, grid, gridExtra, igraph, jsonlite, magrittr, Matrix,
        parallel, reticulate, Rsamtools, rtracklayer, RColorBrewer,
        SingleCellExperiment, SummarizedExperiment, scater, S4Vectors,
        scuttle, stats, scran, stringr, MultiAssayExperiment, tidyr,
        utils, withr, zlibbioc, future, methods
Suggests: BiocStyle, GEOquery, knitr, rmarkdown, markdown,
        BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
LinkingTo: Rcpp, Rhtslib, zlibbioc
SystemRequirements: GNU make, C++17
RoxygenNote: 7.2.3
VignetteBuilder: knitr
URL: https://github.com/OliverVoogd/FLAMES
Config/testthat/edition: 3
Depends: R (>= 2.10)
LazyData: true
StagedInstall: no
git_url: https://git.bioconductor.org/packages/FLAMES
git_branch: RELEASE_3_18
git_last_commit: 8b72098
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: yes
Packaged: 2023-10-24 21:10:47 UTC; biocbuild
Author: Luyi Tian [aut],
  Changqing Wang [aut],
  Youpei You [aut],
  Oliver Voogd [aut, cre],
  Jakob Schuster [aut],
  Shian Su [aut],
  Matthew Ritchie [ctb]
Maintainer: Oliver Voogd <voogd.o@wehi.edu.au>
Built: R 4.3.1; x86_64-apple-darwin20; 2023-10-25 04:46:24 UTC; unix
