FLAMES
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Bioconductor version: 3.23 · Package version: 2.6.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FLAMES")Details
| Maintainer | Changqing Wang <wang.ch@wehi.edu.au> |
| Author | Changqing Wang [aut, cre], Luyi Tian [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Yair D.J. Prawer [aut], Yupei You [aut], Matthew Ritchie [ctb] |
| License | GPL (>= 3) |
| URL | https://mritchielab.github.io/FLAMES |
| Bug Reports | https://github.com/mritchielab/FLAMES/issues |
| System Requirements | GNU make, C++17 |
| Downloads rank | 298 |
| Source branch | RELEASE_3_23 |
| biocViews | AlternativeSplicing, DataImport, DifferentialSplicing, GeneExpression, LongRead, RNASeq, SingleCell, Software, Transcriptomics |
Documentation
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Dependencies
Depends: R (>= 4.2.0)
Imports: abind, basilisk, bambu, BiocParallel, Biostrings, BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli, dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments, Seqinfo, ggplot2, grid, gridExtra, igraph, jsonlite, magrittr, magick, Matrix, MatrixGenerics, readr, reticulate, Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays, ShortRead, SingleCellExperiment, SummarizedExperiment, SpatialExperiment, scater, scatterpie, scrapper (>= 1.5.17), S4Vectors, scuttle, stats, scran, stringr, tidyr, utils, withr, methods, tibble, tidyselect, IRanges
LinkingTo: Rcpp, Rhtslib, testthat
Suggests: BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot, testthat (>= 3.0.0), xml2