FLAMES

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see FLAMES.

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

Bioconductor version: 3.16

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")):

Installation

To install this package, start R (version "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version	1.4.3
In Bioconductor since	BioC 3.14 (R-4.1) (2.5 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
System Requirements	GNU make, C++11
URL	https://github.com/OliverVoogd/FLAMES

Suggests	BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
Linking To	Rcpp, Rhtslib, zlibbioc
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_1.4.3.tar.gz
Windows Binary	FLAMES_1.4.3.zip (64-bit only)
macOS Binary (x86_64)	FLAMES_1.4.3.tgz
macOS Binary (arm64)	FLAMES_1.4.3.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
Old Source Packages for BioC 3.16	Source Archive