This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

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

FLAMES

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

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

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

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

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FLAMES")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FLAMES")
FLAMES HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL (>= 2)
Depends
Imports basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, 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
Linking To Rcpp, Rhtslib, zlibbioc
Suggests BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
System Requirements GNU make, C++11
Enhances
URL https://github.com/OliverVoogd/FLAMES
See More
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 FLAMES_1.6.0.tar.gz
Windows Binary FLAMES_1.6.0.zip (64-bit only)
macOS Binary (x86_64) FLAMES_1.6.0.tgz
macOS Binary (arm64) FLAMES_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FLAMES
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/
Package Downloads Report Download Stats