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✨
card.svg |card.png
FLAMES/json (API)
NEWS

# 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:

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

rnaseqsinglecelltranscriptomicsdataimportdifferentialsplicingalternativesplicinggeneexpressionlongreadrustcargozlibcurlbzip2xz-utilscpp

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.

TargetResultTimeFilesSyslog
bioc-checksNOTE421
linux-devel-arm64NOTE1999
linux-devel-x86_64NOTE2193
source / vignettesOK1478
linux-release-arm64NOTE2041
linux-release-x86_64NOTE2172
macos-release-arm64NOTE1292
macos-release-x86_64NOTE2990
macos-oldrel-arm64NOTE1819
macos-oldrel-x86_64NOTE3887
windows-develFAIL177
windows-releaseFAIL182
windows-oldrelFAIL194
wasm-releaseFAIL259

Exports:add_gene_countsannotation_to_fastabarcode_groupbarcode_segmentblazebulk_long_pipelineBulkPipelinecombine_sceconfigconfig<-controllerscontrollers<-convolution_filtercreate_configcreate_sce_from_dircreate_se_from_dircreate_specutadaptdemultiplex_sockeyeexample_pipelineexperimentfilter_annotationfilter_coveragefind_barcodefind_binfind_diversityfind_variantsflexiplexget_coverageindex_genomeload_configMultiSampleSCPipelinemutation_positionsplot_coverageplot_demultiplexplot_demultiplex_rawplot_durationsplot_isoform_heatmapplot_isoform_reduced_dimplot_isoformsplot_spatial_featureplot_spatial_isoformresume_FLAMESrun_FLAMESrun_stepsc_DTU_analysissc_genotypesc_impute_transcriptsc_long_multisample_pipelinesc_long_pipelinesc_mutationssc_plot_genotypeshowSingleCellPipelinestepssteps<-weight_transcripts

Dependencies:abindAnnotationDbiaskpassassortheadbambubase64encbasiliskbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64bitopsblobblusterbrioBSgenomecachemCairocallrcigarillocirclizeclicliprclueclustercodetoolscollectionscolorspaceComplexHeatmapcowplotcpp11crayoncrewcurldata.tableDBIdbplyrDelayedArraydeldirdescdiffobjdigestdir.expirydoParalleldplyrdqrngedgeRevaluatefarverfastmapfilelockFNNforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggbeeswarmggforceggfunggplot2ggrastrggrepelGlobalOptionsgluegridExtragtableherehmshttrhttr2hwriterigraphinterpIRangesirlbaisobanditeratorsjpegjsonliteKEGGRESTlabelinglambda.rlaterlatticelatticeExtralifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmimemirainanonextopensslotelpheatmappillarpkgbuildpkgconfigpkgloadpngpolyclippraiseprettyunitsprocessxprogresspromisespspurrrpwalignR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRcppTOMLRCurlreadrrestfulrreticulateRhtslibRigraphlibrjsonrlangrprojrootRsamtoolsRSpectraRSQLitersvdrtracklayerRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscatterpiescranscrapperscuttleSeqinfoshapeShortReadSingleCellExperimentsitmosnowSparseArraySpatialExperimentstatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyrtidyselecttweenrtzdbUCSC.utilsutf8uwotvctrsviporviridisviridisLitevroomwaldowithrxgboostXMLXVectoryamlyulab.utils

FLAMES 2.3.1

Changqing Wang, Oliver Voogd, Yupei You

Rendered fromFLAMES_vignette.Rmdusingknitr::rmarkdownon Jun 05 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Add gene counts to a 'SingleCellExperiment' objectadd_gene_counts
GTF/GFF to FASTA conversionannotation_to_fasta
Create a Flexiplex barcode groupbarcode_group
Create a Flexiplex barcode segmentbarcode_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 processingBulkPipeline
Combine SCEcombine_sce
Get pipeline configurationsconfig config,FLAMES.Pipeline-method
Set pipeline configurationsconfig<- config<-,FLAMES.Pipeline-method
Get controllerscontrollers controllers,FLAMES.Pipeline-method
Set controllerscontrollers<- controllers<-,FLAMES.Pipeline-method
Convolution filter for smoothing transcript coveragesconvolution_filter
Create Configuration File From Argumentscreate_config
Create 'SingleCellExperiment' object from 'FLAMES' output foldercreate_sce_from_dir
Create 'SummarizedExperiment' object from 'FLAMES' output foldercreate_se_from_dir
Create a SpatialExperiment objectcreate_spe
cutadapt wrappercutadapt
Demultiplex reads using Sockeye outputsdemultiplex_sockeye
Example pipelinsexample_pipeline
Get pipeline resultsexperiment experiment,FLAMES.Pipeline-method
filter annotation for plotting coveragesfilter_annotation
Filter transcript coveragefilter_coverage
Match Cell Barcodesfind_barcode
Find path to a binary Wrapper for Sys.which to find path to a binaryfind_bin
Compute Gene Isoform Entropy Matrixfind_diversity
bulk variant identificationfind_variants
FLAMES: full-length analysis of mutations and splicingFLAMES
Rcpp port of flexiplexflexiplex
Get read coverages from BAM fileget_coverage
Index the reference genome for minimap2index_genome index_genome,FLAMES.Pipeline-method
Load Configurationsload_config
Pipeline for multi-sample long-read scRNA-seq dataMultiSampleSCPipeline
Calculate mutation positions within the gene bodymutation_positions
plot read coveragesplot_coverage
Plot Cell Barcode demultiplex statisticsplot_demultiplex plot_demultiplex,FLAMES.SingleCellPipeline-method
Plot pipeline step durationsplot_durations plot_durations,FLAMES.Pipeline-method
FLAMES heetmap plotsplot_isoform_heatmap
FLAMES isoform reduced dimensions plotsplot_isoform_reduced_dim
Plot isoformsplot_isoforms
Plot feature on spatial imageplot_spatial_feature
Plot spatial pie chart of isoformsplot_spatial_isoform
Gene quantificationquantify_gene
Resume a FLAMES pipelineresume_FLAMES resume_FLAMES,FLAMES.Pipeline-method
Execute a FLAMES pipelinerun_FLAMES run_FLAMES,FLAMES.Pipeline-method
Execute a single step of the FLAMES pipelinerun_step run_step,FLAMES.Pipeline-method
FLAMES Differential Transcript Usage Analysissc_DTU_analysis
Genotype a single-cell mutationsc_genotype
Impute missing transcript countssc_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 datasc_mutations
Plot genotype of single-cell datasc_plot_genotype
scMixology short-read gene counts - sample 2scmixology_lib10
scMixology long-read transcript counts - sample 2scmixology_lib10_transcripts
scMixology short-read gene counts - sample 1scmixology_lib90
Pipeline for Single Cell DataSingleCellPipeline
Steps to perform in the pipelinesteps steps,FLAMES.Pipeline-method
Set steps to perform in the pipelinesteps<- steps<-,FLAMES.Pipeline-method
Weight transcripts by read countsweight_transcripts