FLAMES
This is the development version of FLAMES; for the stable release version, see FLAMES.
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Bioconductor version: Development (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("FLAMES")):
Installation
To install this package, start R (version "4.5") 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.
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 | 2.1.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0) |
| Imports | basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, DropletUtils, GenomicRanges, GenomicFeatures, txdbmaker, GenomicAlignments, GenomeInfoDb, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite, magrittr, Matrix, MatrixGenerics, parallel, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, 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.
| Source Package | FLAMES_2.1.1.tar.gz |
| Windows Binary (x86_64) | |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/FLAMES/ |
| Package Short Url | https://bioconductor.org/packages/FLAMES/ |
| Package Downloads Report | Download Stats |