FLAMES
This is the released version of FLAMES; for the devel version, see FLAMES.
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Bioconductor version: Release (3.23)
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: Changqing Wang [aut, cre], Luyi Tian [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Yair D.J. Prawer [aut], Yupei You [aut], Matthew Ritchie [ctb]
Maintainer: Changqing Wang <wang.ch at wehi.edu.au>
citation("FLAMES")):Changqing Wang, Luyi Tian, Oliver Voogd, Jakob Schuster, Shian Su, Yair D.J. Prawer, Yupei You. FLAMES: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data. doi:10.18129/B9.bioc.FLAMES, R package version 2.6.0, https://bioconductor.org/packages/FLAMES.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.2.0) |
| Imports | abind, basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli, dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments, Seqinfo, ggplot2, grid, gridExtra, igraph, jsonlite, magrittr, magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays, ShortRead, SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, scrapper (>= 1.5.17), S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, methods, tibble, tidyselect, IRanges |
| System Requirements | GNU make, C++17 |
| URL | https://mritchielab.github.io/FLAMES |
| Bug Reports | https://github.com/mritchielab/FLAMES/issues |
See More
| Suggests | BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot, testthat (>= 3.0.0), xml2 |
| Linking To | Rcpp, Rhtslib, testthat |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | FLAMES_2.6.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | FLAMES_2.6.0.tgz |
| macOS Binary (sonoma-arm64) | FLAMES_2.6.0.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 |