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 (3.17)

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 "4.3") 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

PDF		Reference Manual

Details

biocViews	AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics
Version	1.5.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL (>= 2)
Depends
Imports	basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, 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, jsonlite, parallel, DropletUtils
LinkingTo	Rcpp, Rhtslib, zlibbioc
Suggests	BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0)
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
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/FLAMES/
Package Downloads Report	Download Stats