FLAMES

DOI: 10.18129/B9.bioc.FLAMES    

This package is for version 3.14 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: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	FLAMES
HTML	R Script	Vignette for FLAMES on Windows
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version	1.0.2
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	GPL (>= 2)
Depends
Imports	basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, Rsamtools, utils, zlibbioc, scater, dplyr, tidyr, magrittr, S4Vectors, scuttle, stats
LinkingTo	Rcpp, Rhtslib, zlibbioc
Suggests	BiocStyle, knitr, rmarkdown, markdown, BiocFileCache
SystemRequirements	GNU make, C++11
Enhances
URL	https://github.com/OliverVoogd/FLAMES
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_1.0.2.tar.gz
Windows Binary	FLAMES_1.0.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	FLAMES_1.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FLAMES
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FLAMES
Package Short Url	https://bioconductor.org/packages/FLAMES/
Package Downloads Report	Download Stats