DOI: 10.18129/B9.bioc.FLAMES    

This is the development version of FLAMES; for the stable release version, see FLAMES.

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

Bioconductor version: Development (3.17)

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

Maintainer: Voogd Oliver <voogd.o at wehi.edu.au>

Citation (from within R, enter citation("FLAMES")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version 1.5.0
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
License GPL (>= 2)
Imports basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, Rsamtools, utils, zlibbioc, scater, dplyr, tidyr, magrittr, S4Vectors, scuttle, stats, rtracklayer, igraph, ggbio, GenomicRanges, Matrix, BiocGenerics, ggplot2, scran, ComplexHeatmap, RColorBrewer, circlize, grid, gridExtra, cowplot, stringr, bambu, GenomeInfoDb, withr, Biostrings, GenomicFeatures, jsonlite, parallel, DropletUtils
LinkingTo Rcpp, Rhtslib, zlibbioc
Suggests BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
SystemRequirements GNU make, C++11
URL https://github.com/OliverVoogd/FLAMES
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/FLAMES
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FLAMES
Package Short Url https://bioconductor.org/packages/FLAMES/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: