FLAMES
This package is for version 3.14 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: 3.14
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 "4.1") 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 |
Vignette for FLAMES on Windows | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics |
Version | 1.0.2 |
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 |
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_1.0.2.tar.gz |
Windows Binary | FLAMES_1.0.2.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | FLAMES_1.0.2.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 3.14 | Source Archive |