Package: FLAMES 1.11.0

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:Luyi Tian [aut], Changqing Wang [aut, cre], Yupei You [aut], Oliver Voogd [aut], Jakob Schuster [aut], Shian Su [aut], Matthew Ritchie [ctb]

FLAMES_1.11.0.tar.gz

FLAMES_1.11.0.tgz(r-4.4-x86_64)FLAMES_1.11.0.tgz(r-4.3-x86_64)
FLAMES_1.11.0.tar.gz(r-4.5-noble)FLAMES_1.11.0.tar.gz(r-4.4-noble)
FLAMES.pdf |FLAMES.html✨
FLAMES/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:FLAMES-1.11.0(bioc 3.20)FLAMES-1.10.0(bioc 3.19)

bioconductor-package

29 exports 2.50 score 247 dependencies 2 mentions

Last updated 2 months agofrom:7d0c2633b4

Exports:annotation_to_fastablazebulk_long_pipelinecombine_scecreate_configcreate_sce_from_dircreate_se_from_dircutadaptdemultiplex_sockeyefilter_annotationfind_barcodefind_isoformfind_variantsflexiplexget_GRangesListminimap2_alignminimap2_realignparse_gff_treeplot_coverageplot_demultiplexquantify_transcriptsc_DTU_analysissc_heatmap_expressionsc_long_multisample_pipelinesc_long_pipelinesc_mutationssc_reduce_dimssc_umap_expressionsys_which

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbambubase64encbasiliskbasilisk.utilsbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularbiomaRtBiostringsbiovizBasebitbit64bitopsblobblusterbriobroombroom.helpersBSgenomebslibcachemCairocallrcheckmatecirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdescdichromatdiffobjdigestdir.expirydoParalleldplyrdqrngDropletUtilsedgeRensembldbevaluatefansifarverfastmapfilelockFNNfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongGGallyggbeeswarmggbioggplot2ggrastrggrepelggstatsGlobalOptionsglobalsgluegraphgridExtragtablehavenHDF5ArrayherehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglabelledlambda.rlatticelazyevallifecyclelimmalistenvlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimeMultiAssayExperimentmunsellnlmennetopensslOrganismDbiparallellypatchworkpheatmappillarpkgbuildpkgconfigpkgloadplogrplyrpngpraiseprettyunitsprocessxprogressProtGenericspspurrrR.methodsS3R.ooR.utilsR6raggrappdirsRBGLRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLRCurlreadrrematch2reshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartrprojrootRsamtoolsRSpectraRSQLiterstudioapirsvdrtracklayerRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscranscuttleshapeSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytextxdbmakertzdbUCSC.utilsutf8uwotVariantAnnotationvctrsviporviridisviridisLitevroomwaldowithrxfunxgboostXMLxml2XVectoryamlzlibbioc

Readme and manuals

Help Manual

Help pageTopics
GTF/GFF to FASTA conversionannotation_to_fasta
BLAZE Assign reads to cell barcodes.blaze
Pipeline for Bulk Databulk_long_pipeline
Combine SCEcombine_sce
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
cutadapt wrappercutadapt
Demultiplex reads using Sockeye outputsdemultiplex_sockeye
filter annotation for plotting coveragesfilter_annotation
Match Cell Barcodesfind_barcode
Isoform identificationfind_isoform
bulk variant identificationfind_variants
FLAMES: full-length analysis of mutations and splicingFLAMES
Rcpp port of flexiplexflexiplex
Parse FLAMES' GFF outputget_GRangesList
Minimap2 Align to Genomeminimap2_align
Minimap2 re-align reads to transcriptomeminimap2_realign
Parse Gff3 fileparse_gff_tree
plot read coveragesplot_coverage
Plot Cell Barcode demultiplex statisticsplot_demultiplex
Gene quantificationquantify_gene
Transcript quantificationquantify_transcript
FLAMES Differential Transcript Usage Analysissc_DTU_analysis
FLAMES heetmap plotssc_heatmap_expression
Pipeline for Multi-sample Single Cell Datasc_long_multisample_pipeline
Pipeline for Single Cell Datasc_long_pipeline
Variant count for single-cell datasc_mutations
runPCA and runUMAP wrappersc_reduce_dims
FLAMES UMAP plotssc_umap_expression
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
Sys.which wrapper Wrapper for Sys.which that replaces "" with NAsys_which