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 (3.23)

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: Changqing Wang [aut, cre], Luyi Tian [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Yair D.J. Prawer [aut], Yupei You [aut], Matthew Ritchie [ctb]

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

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

Installation

To install this package, start R (version "4.6") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics
Version	2.5.2
In Bioconductor since	BioC 3.14 (R-4.1) (4.5 years)
License	GPL (>= 3)
Depends	R (>= 4.2.0)
Imports	abind, basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli, dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments, Seqinfo, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays, ShortRead, SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, methods, tibble, tidyselect, IRanges
System Requirements	GNU make, C++17
URL	https://mritchielab.github.io/FLAMES
Bug Reports	https://github.com/mritchielab/FLAMES/issues

Suggests	BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot, testthat (>= 3.0.0), xml2
Linking To	Rcpp, Rhtslib, testthat
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	FLAMES_2.5.2.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (big-sur-arm64)
macOS Binary (sonoma-arm64)
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