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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 (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics
Version 1.9.2
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
URL https://github.com/OliverVoogd/FLAMES
Bug Reports https://github.com/mritchielab/FLAMES/issues
See More
Suggests txdbmaker, BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2
Linking To Rcpp, Rhtslib, zlibbioc, 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_1.9.2.tar.gz
Windows Binary
macOS Binary (x86_64) FLAMES_1.9.2.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/FLAMES/
Package Short Url https://bioconductor.org/packages/FLAMES/
Package Downloads Report Download Stats