FLAMES
This package is for version 3.18 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: 3.18
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], Youpei You [aut], Oliver Voogd [aut, cre], Jakob Schuster [aut], Shian Su [aut], Matthew Ritchie [ctb]
Maintainer: Oliver Voogd <voogd.o at wehi.edu.au>
citation("FLAMES")):
Installation
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.
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 | 1.8.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10) |
| Imports | basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, 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 |
| System Requirements | GNU make, C++17 |
| URL | https://github.com/OliverVoogd/FLAMES |
See More
| Suggests | BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0) |
| Linking To | Rcpp, Rhtslib, zlibbioc |
| 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_1.8.0.tar.gz |
| Windows Binary | FLAMES_1.7.3.zip |
| macOS Binary (x86_64) | FLAMES_1.8.0.tgz |
| macOS Binary (arm64) | FLAMES_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FLAMES |
| Source Repository (Developer Access) | git clone [email protected]:packages/FLAMES |
| Bioc Package Browser | https://code.bioconductor.org/browse/FLAMES/ |
| Package Short Url | https://bioconductor.org/packages/FLAMES/ |
| Package Downloads Report | Download Stats |