FLAMES

This package is for version 3.19 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: 3.19

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, cre], Yupei You [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Matthew Ritchie [ctb]

Maintainer: Changqing Wang <wang.ch at wehi.edu.au>

Citation (from within R, enter citation("FLAMES")):

Installation

To install this package, start R (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics

Version 1.10.3

In Bioconductor since BioC 3.14 (R-4.1) (3 years)

License GPL (>= 3)

Depends R (>= 4.1.0)

Imports basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, txdbmaker, 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, tibble, tidyselect, IRanges

System Requirements GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)

URL https://github.com/OliverVoogd/FLAMES

Bug Reports https://github.com/mritchielab/FLAMES/issues

Suggests txdbmaker, BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2

Linking To Rcpp, Rhtslib, zlibbioc, testthat

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package FLAMES_1.10.3.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) FLAMES_1.10.3.tgz

macOS Binary (arm64) FLAMES_1.10.3.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

Old Source Packages for BioC 3.19 Source Archive