FLAMES

DOI: 10.18129/B9.bioc.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 (3.16)

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")

# 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
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version 1.3.3
In Bioconductor since BioC 3.14 (R-4.1) (0.5 years)
License GPL (>= 2)
Depends
Imports basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, Rsamtools, utils, zlibbioc, scater, dplyr, tidyr, magrittr, S4Vectors, scuttle, stats, rtracklayer, igraph, ggbio, GenomicRanges, Matrix, BiocGenerics, ggplot2, scran, ComplexHeatmap, RColorBrewer, circlize, grid, gridExtra, cowplot, stringr, bambu, GenomeInfoDb, withr, Biostrings, GenomicFeatures
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_1.3.3.tar.gz
Windows Binary FLAMES_1.3.3.zip (64-bit only)
macOS 10.13 (High Sierra) FLAMES_1.3.3.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: