Package: musicatk 2.7.0

Joshua D. Campbell

musicatk: Mutational Signature Comprehensive Analysis Toolkit

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Authors:Aaron Chevalier [aut], Natasha Gurevich [aut], Tao Guo [aut], Joshua D. Campbell [aut, cre]

musicatk_2.7.0.tar.gz
musicatk_2.7.0.zip(r-4.7)musicatk_2.7.0.zip(r-4.6)musicatk_2.7.0.zip(r-4.5)
musicatk_2.7.0.tgz(r-4.6-any)musicatk_2.7.0.tgz(r-4.5-any)
musicatk_2.7.0.tar.gz(r-4.7-any)musicatk_2.7.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
musicatk/json (API)

# Install 'musicatk' in R:

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

Bug tracker:https://github.com/campbio/musicatk/issues

Datasets:

cosmic_v2_sigs - COSMIC v2 SBS96 Signatures Result Object
cosmic_v3_dbs_sigs - COSMIC v3 DBS Genome Signatures Result Object
cosmic_v3_indel_sigs - COSMIC v3 Indel Genome Signatures Result Object
cosmic_v3_sbs_sigs - COSMIC v3 SBS96 Genome Signatures Result Object
cosmic_v3_sbs_sigs_exome - COSMIC v3 SBS96 Exome Signatures Result Object
dbs_musica - Dbs_musica
indel_musica - Indel_musica
musica - Musica
musica_annot - Musica_annot
musica_sbs96 - Musica_sbs96
musica_sbs96_tiny - Musica_sbs96_tiny
rep_range - Replication Timing Data as GRanges Object
res - Res
res_annot - Res_annot

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

software biologicalquestion somaticmutation variantannotation

6.74 score 16 stars 17 scripts 88 exports 269 dependencies

Last updated from:4eabe7f8ae. Checks:1 WARNING, 7 NOTE, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	477
linux-devel-x86_64	NOTE	1094
source / vignettes	OK	861
linux-release-x86_64	NOTE	1094
macos-release-arm64	NOTE	629
macos-oldrel-arm64	NOTE	527
windows-devel	NOTE	797
windows-release	NOTE	890
windows-oldrel	NOTE	799
wasm-release	FAIL	516

Exports:%>%add_flank_to_variants add_result annotate_replication_strand annotate_transcript_strand annotate_variant_length annotate_variant_type auto_predict_grid build_custom_table build_standard_table built_tables cluster_exposure combine_count_tables combine_predict_grid compare_cosmic_v2 compare_cosmic_v3 compare_k_vals compare_results cosmic_v2_subtype_map create_musica_from_counts create_musica_from_variants create_umap credible_intervals credible_intervals<-discover_signatures drop_annotation exposure_differential_analysis exposures exposures<-extract_count_tables extract_variants extract_variants_from_maf extract_variants_from_maf_file extract_variants_from_matrix extract_variants_from_vcf extract_variants_from_vcf_file generate_result_grid get_count_table get_modality get_model get_result_list_entry hyperparameter hyperparameter<-k_select metrics metrics<-modality modality<-model_id model_id<-musicatk name_signatures num_signatures num_signatures<-other_parameters other_parameters<-parameter parameter<-plot_cluster plot_differential_analysis plot_exposures plot_heatmap plot_k_comparison plot_sample_counts plot_sample_reconstruction_error plot_signatures plot_umap predict_exposure rc result_list result_list<-samp_annot samp_annot<-sample_names select_genome signatures signatures<-subset_musica_by_annotation subset_musica_by_counts subset_variant_by_type subset_variants_by_samples table_selected tables tables<-umap umap<-variants variants<-

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob boot broom BSgenome BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 BSgenome.Mmusculus.UCSC.mm9 bslib cachem callr car carData cellranger cigarillo circlize cli clipr clue cluster codetools colorspace combinat commonmark ComplexHeatmap conflicted corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr decompTumor2Sig DelayedArray dendextend Deriv digest DNAcopy doBy doParallel dplyr dqrng DT dtplyr ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap flashClust FNN fontawesome forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options gargle generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggsci ggseqlogo ggsignif ggtext GlobalOptions glue googledrive googlesheets4 gridBase gridExtra gridtext gtable gtools haven highr hms htmltools htmlwidgets httpuv httr ids IRanges irlba isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle litedown lme4 lmtest lubridate maftools magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats matrixTests MCMCprecision memoise mgcv mime minqa modelr modeltools multcompView mvtnorm nlme nloptr NLP NMF nnet numDeriv openssl otel pbkrtest pheatmap philentropy pillar pkgconfig plotly plyr png polynom poorman prettyunits processx progress promises ps purrr quadprog quantreg R6 ragg rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppParallel RcppProgress RCurl Rdpack readr readxl reformulas registry rematch rematch2 reprex reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools Rsamtools RSpectra RSQLite rstatix rstudioapi rtracklayer rvest S4Arrays S4Vectors S7 sass scales scatterplot3d selectr Seqinfo shape shiny showtext showtextdb sitmo slam snow sourcetools SparseArray SparseM stringi stringr SummarizedExperiment survival sys sysfonts systemfonts textshaping tibble tidyr tidyselect tidyverse timechange timeDate tinytex tm topicmodels TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene tzdb UCSC.utils urca utf8 uuid uwot VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zoo

Mutational Signature Comprehensive Analysis Toolkit

Rendered frommusicatk.Rmdusingknitr::rmarkdown

Last update: 2025-07-16
Started: 2020-10-02

Help page	Topics
Uses a genome object to find context and add it to the variant table	add_flank_to_variants
Load an external model into a musica object	add_result
Add replication strand annotation to SBS variants based on bedgraph file	annotate_replication_strand
Add transcript strand annotation to SBS variants (defined in genes only)	annotate_transcript_strand
Adds an annotation to the input musica's variant table with length of each variant	annotate_variant_length
Annotate variants with variant type ("SBS", "INS", "DEl", "DBS")	annotate_variant_type
Automatic filtering of signatures for exposure prediction gridded across specific annotation	auto_predict_grid
Builds a custom table from specified user variants	build_custom_table
Builds count tables using various mutation type schemas	build_standard_table
Retrieve the names of count_tables from a musica object	built_tables built_tables,musica-method
Perform clustering analysis from a musica result object	cluster_exposure
Combines tables into a single table that can be used for discovery/prediction	combine_count_tables
Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predicted	combine_predict_grid
Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome)	compare_cosmic_v2
Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classes	compare_cosmic_v3
Compare k values	compare_k_vals
Compare two result files to find similar signatures	compare_results
COSMIC v2 SBS96 Signatures Result Object	cosmic_v2_sigs
Input a cancer subtype to return a list of related COSMIC signatures	cosmic_v2_subtype_map
COSMIC v3 DBS Genome Signatures Result Object	cosmic_v3_dbs_sigs
COSMIC v3 Indel Genome Signatures Result Object	cosmic_v3_indel_sigs
COSMIC v3 SBS96 Genome Signatures Result Object	cosmic_v3_sbs_sigs
COSMIC v3 SBS96 Exome Signatures Result Object	cosmic_v3_sbs_sigs_exome
Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures.	count_table-class
Creates a musica object from a mutation count table	create_musica_from_counts
Creates a musica object from a variant table	create_musica_from_variants
Create a UMAP from a model result	create_umap
Retrieve credible_intervals from a result_model, result_collection, or musica object	credible_intervals credible_intervals,musica-method credible_intervals,result_collection-method credible_intervals,result_model-method credible_intervals<- credible_intervals<-,musica,matrix-method credible_intervals<-,result_collection,matrix-method credible_intervals<-,result_model,matrix-method
dbs_musica	dbs_musica
Discover mutational signatures	discover_signatures
Drops a column from the variant table that the user no longer needs	drop_annotation
Compare exposures of annotated samples	exposure_differential_analysis
Retrieve exposures from a result_model, result_collection, or musica object	exposures exposures,musica-method exposures,result_collection-method exposures,result_model-method exposures<- exposures<-,musica,matrix-method exposures<-,result_collection,matrix-method exposures<-,result_model,matrix-method
Extract count tables list from a musica object	extract_count_tables
Extract variants from mutliple objects	extract_variants
Extract variants from a maf object	extract_variants_from_maf
Extracts variants from a maf file	extract_variants_from_maf_file
Extract variants from matrix or data.frame like objects	extract_variants_from_matrix
Extracts variants from a VariantAnnotation VCF object	extract_variants_from_vcf
Extracts variants from a vcf file	extract_variants_from_vcf_file
Generate result_grid from musica based on annotation and range of k	generate_result_grid
Retrieve count_table matrix from count_table object	get_count_table
Retrieve a specific modality entry from a musica or result_collection object	get_modality get_modality,musica-method get_modality,result_collection-method
Retrieve model from a musica or result collection object	get_model get_model,musica-method get_model,result_collection-method
Retrieve result_list entry from a musica object	get_result_list_entry get_result_list_entry,musica,character-method
Retrieve hyperparameter from a musica or result_collection object	hyperparameter hyperparameter,musica-method hyperparameter,result_collection-method hyperparameter<- hyperparameter<-,musica,list-method hyperparameter<-,result_collection,list-method
indel_musica	indel_musica
Plots for helping decide number of clusters	k_select
Retrieve metrics from a result_model, result_collection, or musica object	metrics metrics,musica-method metrics,result_collection-method metrics,result_model-method metrics<- metrics<-,musica,SimpleList-method metrics<-,result_collection,SimpleList-method metrics<-,result_model,SimpleList-method
Retrieve modality from a result_model, result_collection, or musica object	modality modality,musica-method modality,result_collection-method modality,result_model-method modality<- modality<-,musica,matrix-method modality<-,result_collection,matrix-method modality<-,result_model,matrix-method
Retrieve model_id from a result_model, result_collection, or musica object	model_id model_id,musica-method model_id,result_collection-method model_id,result_model-method model_id<- model_id<-,musica,matrix-method model_id<-,result_collection,matrix-method model_id<-,result_model,matrix-method
musica	musica
musica_annot	musica_annot
musica_sbs96	musica_sbs96
musica_sbs96_tiny	musica_sbs96_tiny
The primary object that contains variants, count_tables, and samples annotations	musica-class
Starts the musicatk interactive Shiny app	musicatk
Rename signatures for a model	name_signatures
Retrieve num_signatures from a result_model, result_collection, or musica object	num_signatures num_signatures,musica-method num_signatures,result_collection-method num_signatures,result_model-method num_signatures<- num_signatures<-,musica,matrix-method num_signatures<-,result_collection,matrix-method num_signatures<-,result_model,matrix-method
Retrieve other_parameters from a result_model, result_collection, or musica object	other_parameters other_parameters,musica-method other_parameters,result_collection-method other_parameters,result_model-method other_parameters<- other_parameters<-,musica,matrix-method other_parameters<-,result_collection,matrix-method other_parameters<-,result_model,matrix-method
Retrieve parameter from a musica or result_collection object	parameter parameter,musica-method parameter,result_collection-method parameter<- parameter<-,musica,list-method parameter<-,result_collection,list-method
Visualize clustering results	plot_cluster
Compare exposures of annotated samples	plot_differential_analysis
Display sample exposures with bar, box, or violin plots	plot_exposures
Plot heatmaps using the exposures matrix	plot_heatmap
Plot k comparison	plot_k_comparison
Plot distribution of sample counts	plot_sample_counts
Plot reconstruction error for a sample	plot_sample_reconstruction_error
Plots the mutational signatures	plot_signatures
Plot a UMAP from a musica result	plot_umap
Prediction of exposures in new samples using pre-existing signatures	predict_exposure
Reverse complement of a string using biostrings	rc
Replication Timing Data as GRanges Object	rep_range
res	res
res_annot	res_annot
The Result Collection object that contains modality, input parameters, prior hyperparameters	result_collection-class
Retrieve result_list from a musica object	result_list result_list,musica-method result_list<- result_list<-,musica,SimpleList-method
Object that contains results for a single model	result_model-class
Get or set sample annotations from a musica object	samp_annot samp_annot,musica-method samp_annot<- samp_annot<-,musica,character,vector-method
Retrieve sample names from a musica object	sample_names sample_names,musica-method
Helper function to load common human or mouse genomes	select_genome
Retrieve signatures from a result_model, result_collection, or musica object	signatures signatures,musica-method signatures,result_collection-method signatures,result_model-method signatures<- signatures<-,musica,matrix-method signatures<-,result_collection,matrix-method signatures<-,result_model,matrix-method
Creates a new musica object subsetted to only one value of a sample annotation	subset_musica_by_annotation
Creates a new musica subsetted to only samples with enough variants	subset_musica_by_counts
Subsets a variant table based on Variant Type	subset_variant_by_type
Return sample from musica_variant object	subset_variants_by_samples
Retrieve table name used for plotting from a result_model object	table_selected table_selected,result_model-method
Retrieve the list of count_tables from a musica object	tables tables,musica-method tables<- tables<-,musica,list-method
Retrieve umap list from a result_model, result_collection, or musica object	umap umap,musica-method umap,result_collection-method umap,result_model-method umap<- umap<-,musica,matrix-method umap<-,result_collection,matrix-method umap<-,result_model,matrix-method
Retrieve variants from a musica object	variants variants,musica-method variants<- variants<-,musica,data.table-method

Package: musicatk 2.7.0

musicatk: Mutational Signature Comprehensive Analysis Toolkit

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