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Bioconductor - FLAMES

FLAMES

This is the released version of FLAMES; for the devel version, see FLAMES.

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Bioconductor version: Release (3.21)

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 (from within R, enter citation("FLAMES")): Installation

To install this package, start R (version "4.5") 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")

Details biocViews AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics Version 2.2.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License GPL (>= 3) Depends R (>= 4.2.0) Imports abind, basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, txdbmaker, GenomicAlignments, GenomeInfoDb, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, SparseArray(>= 1.7.7), SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, future, methods, tibble, tidyselect, IRanges System Requirements GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17) URL https://mritchielab.github.io/FLAMES Bug Reports https://github.com/mritchielab/FLAMES/issues See More Suggests BiocStyle, GEOquery, knitr, rmarkdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2 Linking To Rcpp, Rhtslib, 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.

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