Bioconductor version: Release (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: Luyi Tian [aut], Oliver Voogd [aut, cre], Jakob Schuster [aut], Changqing Wang [aut], Shian Su [aut], Matthew Ritchie [ctb]
Maintainer: Oliver Voogd <voogd.o at wehi.edu.au>
Citation (from within R,
enter citation("FLAMES")
):
To install this package, start R (version "4.3") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FLAMES")
HTML | R Script | FLAMES |
Reference Manual | ||
Text | NEWS |
biocViews | AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics |
Version | 1.6.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
License | GPL (>= 2) |
Depends | |
Imports | basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, 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 |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | FLAMES_1.6.0.tar.gz |
Windows Binary | FLAMES_1.6.0.zip (64-bit only) |
macOS Binary (x86_64) | FLAMES_1.6.0.tgz |
macOS Binary (arm64) | FLAMES_1.6.0.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 |
Old Source Packages for BioC 3.17 | Source Archive |
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