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DESCRIPTION
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DESCRIPTION
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Package: FLAMES
Type: Package
Title: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Version: 1.9.2
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,
Biostrings,
BiocGenerics,
circlize,
ComplexHeatmap,
cowplot,
dplyr,
DropletUtils,
GenomicRanges,
GenomicFeatures,
txdbmaker,
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,
tibble,
tidyselect,
IRanges
Suggests:
txdbmaker,
BiocStyle,
GEOquery,
knitr,
rmarkdown,
markdown,
BiocFileCache,
R.utils,
ShortRead,
uwot,
testthat (>= 3.0.0),
xml2
LinkingTo: Rcpp, Rhtslib, zlibbioc, testthat
SystemRequirements: GNU make, C++17
RoxygenNote: 7.3.1
VignetteBuilder: knitr
URL: https://github.com/OliverVoogd/FLAMES
Config/testthat/edition: 3
Depends:
R (>= 4.1.0)
LazyData: true
StagedInstall: no