Package: FLAMES 2.1.6

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_2.1.6.tar.gz
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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'))

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

Pkgdown 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-2.1.5(bioc 3.21)FLAMES-2.0.2(bioc 3.20)

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

7.89 score 27 stars 12 scripts 372 downloads 2 mentions 39 exports 248 dependencies

Last updated 2 days agofrom:925331f79f. Checks:1 OK, 1 NOTE, 4 FAILURE, 5 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 15 2025
R-4.5-win-x86_64	ERROR	Feb 15 2025
R-4.5-mac-x86_64	OUTDATED	Feb 10 2025
R-4.5-mac-aarch64	OUTDATED	Feb 10 2025
R-4.5-linux-x86_64	NOTE	Feb 15 2025
R-4.4-win-x86_64	ERROR	Feb 15 2025
R-4.4-mac-x86_64	ERROR	Feb 15 2025
R-4.4-mac-aarch64	ERROR	Feb 15 2025
R-4.3-win-x86_64	ERROR	Feb 15 2025
R-4.3-mac-aarch64	OUTDATED	Feb 06 2025
R-4.3-mac-x86_64	OUTDATED	Jan 07 2025

Exports:add_gene_counts annotation_to_fasta blaze bulk_long_pipeline combine_sce convolution_filter create_config create_sce_from_dir create_se_from_dir create_spe cutadapt demultiplex_sockeye filter_annotation filter_coverage find_barcode find_bin find_isoform find_variants flexiplex get_coverage get_GRangesList minimap2_align minimap2_realign mutation_positions plot_coverage plot_demultiplex plot_isoform_heatmap plot_isoform_reduced_dim plot_isoforms plot_spatial_feature plot_spatial_isoform quantify_transcript quantify_transcript_flames sc_DTU_analysis sc_impute_transcript sc_long_multisample_pipeline sc_long_pipeline sc_mutations weight_transcripts

Dependencies:abind AnnotationDbi AnnotationFilter askpass assorthead backports bambu base64enc basilisk basilisk.utils beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocNeighbors BiocParallel BiocSingular biomaRt Biostrings biovizBase bit bit64 bitops blob bluster brio BSgenome bslib cachem Cairo callr checkmate circlize cli clipr clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats desc dichromat diffobj digest dir.expiry doParallel dplyr dqrng DropletUtils edgeR ensembldb evaluate fansi farver fastmap filelock FNN fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options future generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong GGally ggbeeswarm ggbio ggforce ggfun ggplot2 ggrastr ggrepel ggstats GlobalOptions globals glue graph gridExtra gtable h5mread HDF5Array here highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma listenv locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime munsell nlme nnet openssl OrganismDbi parallelly patchwork pheatmap pillar pkgbuild pkgconfig pkgload plogr plyr png polyclip praise prettyunits processx progress ProtGenerics ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs RBGL RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress RcppTOML RCurl readr reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors sass ScaledMatrix scales scater scatterpie scran scuttle shape SingleCellExperiment sitmo snow SparseArray sparseMatrixStats SpatialExperiment statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tinytex tweenr txdbmaker tzdb UCSC.utils utf8 uwot VariantAnnotation vctrs vipor viridis viridisLite vroom waldo withr xfun xgboost XML xml2 XVector yaml yulab.utils

FLAMES

Oliver Voogd, Changqing Wang, Yupei You

Rendered fromFLAMES_vignette.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2024-09-25
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
BLAZE Assign reads to cell barcodes.	blaze
Pipeline for Bulk Data	bulk_long_pipeline
Combine SCE	combine_sce
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
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
Isoform identification	find_isoform
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
Parse FLAMES' GFF output	get_GRangesList
Minimap2 Align to Genome	minimap2_align
Minimap2 re-align reads to transcriptome	minimap2_realign
Calculate mutation positions within the gene body	mutation_positions
plot read coverages	plot_coverage
Plot Cell Barcode demultiplex statistics	plot_demultiplex
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
Transcript quantification	quantify_transcript
FLAMES Transcript quantification	quantify_transcript_flames
FLAMES Differential Transcript Usage Analysis	sc_DTU_analysis
Impute missing transcript counts	sc_impute_transcript
Pipeline for Multi-sample Single Cell Data	sc_long_multisample_pipeline
Pipeline for Single Cell Data	sc_long_pipeline
Variant count for single-cell data	sc_mutations
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
Weight transcripts by read counts	weight_transcripts