FLAMES
This package is for version 3.19 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: 3.19
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, cre], Yupei You [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Matthew Ritchie [ctb]
Maintainer: Changqing Wang <wang.ch at wehi.edu.au>
citation("FLAMES")
):
Installation
To install this package, start R (version "4.4") 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 | 1.10.3 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
License | GPL (>= 3) |
Depends | R (>= 4.1.0) |
Imports | basilisk, bambu, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, txdbmaker, 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, tibble, tidyselect, IRanges |
System Requirements | GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17) |
URL | https://github.com/OliverVoogd/FLAMES |
Bug Reports | https://github.com/mritchielab/FLAMES/issues |
See More
Suggests | txdbmaker, BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2 |
Linking To | Rcpp, Rhtslib, zlibbioc, 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_1.10.3.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | FLAMES_1.10.3.tgz |
macOS Binary (arm64) | FLAMES_1.10.3.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 |
Old Source Packages for BioC 3.19 | Source Archive |