FLAMES

DOI: 10.18129/B9.bioc.FLAMES    

This is the development version of FLAMES; to use it, please install the devel version of Bioconductor.

FLAMES; Full Length Transcriptome Splicing and Mutation Analysis for Long-Read Data

Bioconductor version: Development (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], 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 "4.1") and enter:

if (!requireNamespace("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")

 

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 0.99.31
In Bioconductor since BioC 3.14 (R-4.1)
License GPL (>= 2)
Depends
Imports basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, Rsamtools, utils, zlibbioc, scater, dplyr, tidyr, magrittr, S4Vectors, scuttle
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_0.99.31.tar.gz
Windows Binary FLAMES_0.99.31.zip (32- & 64-bit)
macOS 10.13 (High Sierra) FLAMES_0.99.31.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

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