Package: FLAMES 2.7.0

Changqing Wang

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

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.

Authors: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]

FLAMES_2.7.0.tar.gz

FLAMES_2.7.0.tgz(r-4.6-x86_64)FLAMES_2.7.0.tgz(r-4.6-arm64)FLAMES_2.7.0.tgz(r-4.5-x86_64)FLAMES_2.7.0.tgz(r-4.5-arm64)
FLAMES_2.7.0.tar.gz(r-4.7-arm64)FLAMES_2.7.0.tar.gz(r-4.7-x86_64)FLAMES_2.7.0.tar.gz(r-4.6-arm64)FLAMES_2.7.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FLAMES/json (API)

# Install 'FLAMES' in R:

install.packages('FLAMES', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mritchielab/flames/issues

Pkgdown/docs site:https://mritchielab.github.io

Uses libs:

zlib– Compression library
curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
c++– GNU Standard C++ Library v3

Datasets:

scmixology_lib10 - ScMixology short-read gene counts - sample 2
scmixology_lib10_transcripts - ScMixology long-read transcript counts - sample 2
scmixology_lib90 - ScMixology short-read gene counts - sample 1

On BioConductor:FLAMES-2.7.0(bioc 3.24)FLAMES-2.6.0(bioc 3.23)

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread rust cargo zlib curl bzip2 xz-utils cpp

8.73 score 63 stars 34 scripts 470 downloads 2 mentions 57 exports 209 dependencies

Last updated from:38fd4e3299. Checks:9 NOTE, 1 OK, 4 FAIL. Indexed: yes.
A new build is currently in progress.

Target	Result	Time
bioc-checks	NOTE	421
linux-devel-arm64	NOTE	1999
linux-devel-x86_64	NOTE	2193
source / vignettes	OK	1478
linux-release-arm64	NOTE	2041
linux-release-x86_64	NOTE	2172
macos-release-arm64	NOTE	1292
macos-release-x86_64	NOTE	2990
macos-oldrel-arm64	NOTE	1819
macos-oldrel-x86_64	NOTE	3887
windows-devel	FAIL	177
windows-release	FAIL	182
windows-oldrel	FAIL	194
wasm-release	FAIL	259

Exports:add_gene_counts annotation_to_fasta barcode_group barcode_segment blaze bulk_long_pipeline BulkPipeline combine_sce config config<-controllers controllers<-convolution_filter create_config create_sce_from_dir create_se_from_dir create_spe cutadapt demultiplex_sockeye example_pipeline experiment filter_annotation filter_coverage find_barcode find_bin find_diversity find_variants flexiplex get_coverage index_genome load_config MultiSampleSCPipeline mutation_positions plot_coverage plot_demultiplex plot_demultiplex_raw plot_durations plot_isoform_heatmap plot_isoform_reduced_dim plot_isoforms plot_spatial_feature plot_spatial_isoform resume_FLAMES run_FLAMES run_step sc_DTU_analysis sc_genotype sc_impute_transcript sc_long_multisample_pipeline sc_long_pipeline sc_mutations sc_plot_genotype show SingleCellPipeline steps steps<-weight_transcripts

Dependencies:abind AnnotationDbi askpass assorthead bambu base64enc basilisk beachmat beeswarm BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster brio BSgenome cachem Cairo callr cigarillo circlize cli clipr clue cluster codetools collections colorspace ComplexHeatmap cowplot cpp11 crayon crew curl data.table DBI dbplyr DelayedArray deldir desc diffobj digest dir.expiry doParallel dplyr dqrng edgeR evaluate farver fastmap filelock FNN foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggbeeswarm ggforce ggfun ggplot2 ggrastr ggrepel GlobalOptions glue gridExtra gtable here hms httr httr2 hwriter igraph interp IRanges irlba isoband iterators jpeg jsonlite KEGGREST labeling lambda.r later lattice latticeExtra lifecycle limma locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mime mirai nanonext openssl otel pheatmap pillar pkgbuild pkgconfig pkgload png polyclip praise prettyunits processx progress promises ps purrr pwalign R.methodsS3 R.oo R.utils R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress RcppTOML RCurl readr restfulr reticulate Rhtslib Rigraphlib rjson rlang rprojroot Rsamtools RSpectra RSQLite rsvd rtracklayer Rtsne S4Arrays S4Vectors S7 ScaledMatrix scales scater scatterpie scran scrapper scuttle Seqinfo shape ShortRead SingleCellExperiment sitmo snow SparseArray SpatialExperiment statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tweenr tzdb UCSC.utils utf8 uwot vctrs vipor viridis viridisLite vroom waldo withr xgboost XML XVector yaml yulab.utils

FLAMES 2.3.1

Rendered fromFLAMES_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-15
Started: 2021-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add gene counts to a 'SingleCellExperiment' object	add_gene_counts
GTF/GFF to FASTA conversion	annotation_to_fasta
Create a Flexiplex barcode group	barcode_group
Create a Flexiplex barcode segment	barcode_segment
BLAZE Assign reads to cell barcodes.	blaze
Pipeline for bulk long read RNA-seq data processing (deprecated)	bulk_long_pipeline
Pipeline for bulk long read RNA-seq data processing	BulkPipeline
Combine SCE	combine_sce
Get pipeline configurations	config config,FLAMES.Pipeline-method
Set pipeline configurations	config<- config<-,FLAMES.Pipeline-method
Get controllers	controllers controllers,FLAMES.Pipeline-method
Set controllers	controllers<- controllers<-,FLAMES.Pipeline-method
Convolution filter for smoothing transcript coverages	convolution_filter
Create Configuration File From Arguments	create_config
Create 'SingleCellExperiment' object from 'FLAMES' output folder	create_sce_from_dir
Create 'SummarizedExperiment' object from 'FLAMES' output folder	create_se_from_dir
Create a SpatialExperiment object	create_spe
cutadapt wrapper	cutadapt
Demultiplex reads using Sockeye outputs	demultiplex_sockeye
Example pipelins	example_pipeline
Get pipeline results	experiment experiment,FLAMES.Pipeline-method
filter annotation for plotting coverages	filter_annotation
Filter transcript coverage	filter_coverage
Match Cell Barcodes	find_barcode
Find path to a binary Wrapper for Sys.which to find path to a binary	find_bin
Compute Gene Isoform Entropy Matrix	find_diversity
bulk variant identification	find_variants
FLAMES: full-length analysis of mutations and splicing	FLAMES
Rcpp port of flexiplex	flexiplex
Get read coverages from BAM file	get_coverage
Index the reference genome for minimap2	index_genome index_genome,FLAMES.Pipeline-method
Load Configurations	load_config
Pipeline for multi-sample long-read scRNA-seq data	MultiSampleSCPipeline
Calculate mutation positions within the gene body	mutation_positions
plot read coverages	plot_coverage
Plot Cell Barcode demultiplex statistics	plot_demultiplex plot_demultiplex,FLAMES.SingleCellPipeline-method
Plot pipeline step durations	plot_durations plot_durations,FLAMES.Pipeline-method
FLAMES heetmap plots	plot_isoform_heatmap
FLAMES isoform reduced dimensions plots	plot_isoform_reduced_dim
Plot isoforms	plot_isoforms
Plot feature on spatial image	plot_spatial_feature
Plot spatial pie chart of isoforms	plot_spatial_isoform
Gene quantification	quantify_gene
Resume a FLAMES pipeline	resume_FLAMES resume_FLAMES,FLAMES.Pipeline-method
Execute a FLAMES pipeline	run_FLAMES run_FLAMES,FLAMES.Pipeline-method
Execute a single step of the FLAMES pipeline	run_step run_step,FLAMES.Pipeline-method
FLAMES Differential Transcript Usage Analysis	sc_DTU_analysis
Genotype a single-cell mutation	sc_genotype
Impute missing transcript counts	sc_impute_transcript
Pipeline for Multi-sample Single Cell Data (deprecated)	sc_long_multisample_pipeline
Pipeline for Single Cell Data (deprecated)	sc_long_pipeline
Variant count for single-cell data	sc_mutations
Plot genotype of single-cell data	sc_plot_genotype
scMixology short-read gene counts - sample 2	scmixology_lib10
scMixology long-read transcript counts - sample 2	scmixology_lib10_transcripts
scMixology short-read gene counts - sample 1	scmixology_lib90
Pipeline for Single Cell Data	SingleCellPipeline
Steps to perform in the pipeline	steps steps,FLAMES.Pipeline-method
Set steps to perform in the pipeline	steps<- steps<-,FLAMES.Pipeline-method
Weight transcripts by read counts	weight_transcripts