FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Bioconductor version: Release (3.19)

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.

Author: Luyi Tian [aut], Changqing Wang [aut, cre], Yupei You [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Matthew Ritchie [ctb]

Maintainer: Changqing Wang <wang.ch at wehi.edu.au>

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Reference Manual PDF


biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL (>= 3)
Depends R (>= 4.1.0)
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
System Requirements GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)
URL https://github.com/OliverVoogd/FLAMES
Bug Reports https://github.com/mritchielab/FLAMES/issues
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Suggests txdbmaker, BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2
Linking To Rcpp, Rhtslib, zlibbioc, testthat
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Source Package FLAMES_1.10.0.tar.gz
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macOS Binary (x86_64) FLAMES_1.10.0.tgz
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Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FLAMES
Bioc Package Browser https://code.bioconductor.org/browse/FLAMES/
Package Short Url https://bioconductor.org/packages/FLAMES/
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