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FLAMES

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


Bioconductor version: Release (3.18)

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], Youpei You [aut], Oliver Voogd [aut, cre], Jakob Schuster [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, LongRead, RNASeq, SingleCell, Software, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL (>= 2)
Depends R (>= 2.10)
Imports basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, 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
System Requirements GNU make, C++17
URL https://github.com/OliverVoogd/FLAMES
See More
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
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Package Archives

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

Source Package FLAMES_1.8.0.tar.gz
Windows Binary FLAMES_1.7.3.zip
macOS Binary (x86_64) FLAMES_1.8.0.tgz
macOS Binary (arm64) FLAMES_1.8.0.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