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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/FLAMES/ |
| Package Short Url | https://bioconductor.org/packages/FLAMES/ |
| Package Downloads Report | Download Stats |