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This is the development version of FLAMES; for the stable release version, see FLAMES.
Bioconductor version: Development (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: 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 (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") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("FLAMES")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual |
biocViews | AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics |
Version | 1.5.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (1 year) |
License | GPL (>= 2) |
Depends | |
Imports | basilisk, reticulate, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, 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, jsonlite, parallel, DropletUtils |
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 | |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/FLAMES |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FLAMES |
Package Short Url | https://bioconductor.org/packages/FLAMES/ |
Package Downloads Report | Download Stats |
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