FLAMES
This package is for version 3.15 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: 3.15
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: Tian Luyi [aut], Voogd Oliver [aut, cre], Schuster Jakob [aut], Wang Changqing [aut], Su Shian [aut], Ritchie Matthew [ctb]
Maintainer: Voogd Oliver <voogd.o at wehi.edu.au>
citation("FLAMES")):
Installation
To install this package, start R (version "4.2") 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, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 years) |
| License | GPL (>= 2) |
| Depends | |
| Imports | basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, Rsamtools, utils, zlibbioc, scater, dplyr, tidyr, magrittr, S4Vectors, scuttle, stats, rtracklayer, igraph, ggbio, GenomicRanges, Matrix, BiocGenerics, ggplot2, scran, ComplexHeatmap, RColorBrewer, circlize, grid, gridExtra, cowplot, stringr, bambu, GenomeInfoDb, withr, Biostrings, GenomicFeatures |
| System Requirements | GNU make, C++11 |
| URL | https://github.com/OliverVoogd/FLAMES |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, BiocFileCache |
| 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_1.2.2.tar.gz |
| Windows Binary | FLAMES_1.2.2.zip (64-bit only) |
| macOS Binary (x86_64) | FLAMES_1.2.2.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 3.15 | Source Archive |