Package: sigvar 0.99.8

Nicolas Alcala

sigvar: Quantify and visualize variability of mutational signatures within and across samples

This package allows users to import mutational signature attribution (a.k.a. exposure) matrices and compute, visualize, and test their variabilities within and across samples.

Authors:Maike Morrison [aut], Nicolas Alcala [aut, cre], Worldwide Cancer Research [fnd], French Ligue Nationale Contre le Cancer [fnd]

sigvar_0.99.8.tar.gz
sigvar_0.99.8.zip(r-4.7-any)sigvar_0.99.8.zip(r-4.6-any)sigvar_0.99.8.zip(r-4.5-any)
sigvar_0.99.8.tgz(r-4.6-any)sigvar_0.99.8.tgz(r-4.5-any)
sigvar_0.99.8.tar.gz(r-4.7-any)sigvar_0.99.8.tar.gz(r-4.6-any)
sigvar_0.99.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sigvar/json (API)

# Install 'sigvar' in R:

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

Bug tracker:https://github.com/maikemorrison/sigvar/issues

Datasets:

all_sig_pal - Color palette for mutational signatures analyzed in the study by Morrison et al.
carcinogens_mice_SBS - Single base substitution signature attributions found in mice exposed to 20 known or suspected carcinogens.
carcinogens_mice_SBS.refs - Reference single base substitution signatures found in mice exposed to 20 known or suspected carcinogens.
COSMIC3.0_ID - Indel reference signatures for COSMIC3.0
COSMIC3.0_SBS - Single base substitution reference signatures for COSMIC3.0
COSMIC3.1_CN - Copy Number reference signatures for COSMIC3.1
COSMIC3.3_CN - Copy Number reference signatures for COSMIC3.3
COSMIC3.3_DBS - Double base reference signatures for COSMIC3.0
COSMIC3.3_DBS_mm10 - Mice Double base reference signatures for COSMIC3.0
COSMIC3.3_ID - Indel reference signatures for COSMIC3.3.1
COSMIC3.3.1_SBS - Single base substitution reference signatures for COSMIC3.3.1
COSMIC3.3.1_SBS_mm10 - Mice Single base substitution reference signatures for COSMIC3.3.1
EGFR_context_counts_ordered - Counts of each context class for the main transcript of gene EGFR
EGFR_drivers_intogen_SBS96 - SBS96 spectrum from the intogen website for gene EGFR in lung adenocarcinomas
ESCC_countries_SBS - Single base substitution signature attributions found in esophageal squamous cell carcinoma across countries with varying incidence.
ESCC_countries_SBS.refs - Reference COSMIC Single base substitution signatures found in esophageal squamous cell carcinoma across countries with varying incidence.
ESCC_sig_activity - Activity of SBS, DBS, and ID mutational signatures in a global sample of esophageal squamous cell carcinoma cases.
ESCC_sig_similarity - Cosine similarity of SBS, DBS, and ID mutational signatures found in a global sample of esophageal squamous cell carcinoma cases.
Intogen_EGFR_LUAD - Driver mutations from the intogen website for gene EGFR in lung adenocarcinomas
MESOMICS_CN_SBS - Copy Number and Single Base Substitution mutational signatures for 120 malignant pleural mesothelioma from the MESOMICS cohort
mutsig_carcinogens_mice_bootstrap_p_vals - Bootstrap p-values comparing SVA results for carcinogen-exposed murine tumors to spontaneous tumors
mutsig_carcinogens_mice_SBS - Single Base Substitution mutational signatures for 181 mice exposed to known or suspected carcinogens
mutsig_carcinogens_mice_SBS.refs - Definitions of murine single base substitution mutational signatures
PCAWG_SigProfiler_COSMIC_DBS - Double Base Substitution COSMIC mutational signatures for 2780 tumors
PCAWG_SigProfiler_COSMIC_ID - Indel COSMIC mutational signatures for 2780 tumors
PCAWG_SigProfiler_COSMIC_SBS - Single Base Substitution COSMIC mutational signatures for 2780 tumors
radiation_sigs_morton - Single base substitution signature attributions found in papillary thyroid carcinoma from Chernobyl incident survivors.
radiation_sigs_morton_cossim - Cosine similarity matrix of Single base substitution signatures found in papillary thyroid carcinoma from Chernobyl incident survivors.
rcc_sig_activity - Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.
rcc_sim - Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.
sbs_palette - Single Base Substitution COSMIC mutational signatures for 2780 tumors
Sherlock_LCINS_SBS - Single base substitution signature attributions found in Lung cancer in never smokers.
Sherlock_LCINS_SBS.refs - Reference COSMIC Single base substitution signatures found in Lung cancer in never smokers.
Sherlock_LCINS.metadata - Metadata accompanying mutational signatures for lung cancer in never smokers.
smoker_sigs_chen - Activity of Smoking, APOBEC, and Ageing mutational signatures in a sample of East Asian lung adenocarcinoma patients.
smoker_sigs_chen_cossim - Cosine similarity of smoking, APOBEC, and ageing mutational signatures found in a sample of East Asian lung adenocarcinoma patients.
TP53_context_counts_ordered - Counts of each context class for the main transcript of gene TP53
TP53_drivers_intogen_LUAD - Driver mutations from the intogen website for gene TP53 in lung adenocarcinomas
TP53_drivers_intogen_SBS96 - SBS96 spectrum from the intogen website for gene TP53 in lung adenocarcinomas
zhang_sig_activity - Activity of SBS mutational signatures in samples of lung cancer in never smokers
zhang_sig_similarity - Cosine similarity of SBS mutational signatures found in samples of lung cancer in never smokers

On BioConductor:sigvar-0.99.8(bioc 3.24)

software wholegenome somaticmutation structuralvariation statisticalmethod visualization drivermutation dataimport

5.43 score 3 stars 8 scripts 139 downloads 15 exports 107 dependencies

Last updated from:df8143da9e. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	242
linux-devel	OK	474
source / vignettes	OK	410
linux-release	OK	457
macos-release	OK	357
macos-oldrel	OK	307
windows-devel	OK	364
windows-release	OK	323
windows-oldrel	OK	348
wasm-release	OK	200

Exports:cossim fst fst_norm get_SBS96_driver_spectrum get_SBS96_spectrum het het_mean het_pooled import_SigProfiler plot_dots plot_SBS_spectrum plot_signature_prop sigboot sigvar time_weights

Dependencies:AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli clipr codetools commonmark cpp11 crayon curl DBI dplyr farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggh4x ggplot2 ggtext glue gridtext gtable hms httr IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lifecycle litedown magrittr markdown MASS matrixStats memoise mime openssl pillar pkgconfig png polyclip prettyunits progress purrr R6 RColorBrewer Rcpp RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors S7 scales Seqinfo snow stringi stringr sys systemfonts tibble tidyr tidyselect tweenr TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 XVector yaml

Introduction to Signature Variability Analysis with sigvar

Rendered fromsigvar_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-07-17
Started: 2026-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Color palette for mutational signatures analyzed in the study by Morrison et al.	all_sig_pal
Single base substitution signature attributions found in mice exposed to 20 known or suspected carcinogens.	carcinogens_mice_SBS
Reference single base substitution signatures found in mice exposed to 20 known or suspected carcinogens.	carcinogens_mice_SBS.refs
Indel reference signatures for COSMIC3.0	COSMIC3.0_ID
Single base substitution reference signatures for COSMIC3.0	COSMIC3.0_SBS
Copy Number reference signatures for COSMIC3.1	COSMIC3.1_CN
Copy Number reference signatures for COSMIC3.3	COSMIC3.3_CN
Double base reference signatures for COSMIC3.0	COSMIC3.3_DBS
Mice Double base reference signatures for COSMIC3.0	COSMIC3.3_DBS_mm10
Indel reference signatures for COSMIC3.3.1	COSMIC3.3_ID
Single base substitution reference signatures for COSMIC3.3.1	COSMIC3.3.1_SBS
Mice Single base substitution reference signatures for COSMIC3.3.1	COSMIC3.3.1_SBS_mm10
Compute the cosine similarity matrix for a set of mutational signatures.	cossim
Counts of each context class for the main transcript of gene EGFR	EGFR_context_counts_ordered
SBS96 spectrum from the intogen website for gene EGFR in lung adenocarcinomas	EGFR_drivers_intogen_SBS96
Single base substitution signature attributions found in esophageal squamous cell carcinoma across countries with varying incidence.	ESCC_countries_SBS
Reference COSMIC Single base substitution signatures found in esophageal squamous cell carcinoma across countries with varying incidence.	ESCC_countries_SBS.refs
Activity of SBS, DBS, and ID mutational signatures in a global sample of esophageal squamous cell carcinoma cases.	ESCC_sig_activity
Cosine similarity of SBS, DBS, and ID mutational signatures found in a global sample of esophageal squamous cell carcinoma cases.	ESCC_sig_similarity
Compute the Fst of a matrix of compositional vectors	fst
Compute the normalized Fst of a matrix of compositional vectors	fst_norm
get_SBS96_driver_spectrum	get_SBS96_driver_spectrum
get_SBS96_spectrum	get_SBS96_spectrum
Compute the Gini-Simpson index of a compositional vector	het
Compute the mean Gini-Simpson index of the rows in a matrix of compositional vectors	het_mean
Compute the pooled Gini-Simpson index of the rows in a matrix of compositional vectors	het_pooled
import_SigProfiler	import_SigProfiler
Driver mutations from the intogen website for gene EGFR in lung adenocarcinomas	Intogen_EGFR_LUAD
Copy Number and Single Base Substitution mutational signatures for 120 malignant pleural mesothelioma from the MESOMICS cohort	MESOMICS_CN_SBS
Bootstrap p-values comparing SVA results for carcinogen-exposed murine tumors to spontaneous tumors	mutsig_carcinogens_mice_bootstrap_p_vals
Single Base Substitution mutational signatures for 181 mice exposed to known or suspected carcinogens	mutsig_carcinogens_mice_SBS
Definitions of murine single base substitution mutational signatures	mutsig_carcinogens_mice_SBS.refs
Double Base Substitution COSMIC mutational signatures for 2780 tumors	PCAWG_SigProfiler_COSMIC_DBS
Indel COSMIC mutational signatures for 2780 tumors	PCAWG_SigProfiler_COSMIC_ID
Single Base Substitution COSMIC mutational signatures for 2780 tumors	PCAWG_SigProfiler_COSMIC_SBS
Plot the mean mutational signature activities of each group of samples	plot_dots
Plot an SBS mutational spectrum	plot_SBS_spectrum
Visualize a relative abundance matrix as a stacked bar plot.	plot_signature_prop
Single base substitution signature attributions found in papillary thyroid carcinoma from Chernobyl incident survivors.	radiation_sigs_morton
Cosine similarity matrix of Single base substitution signatures found in papillary thyroid carcinoma from Chernobyl incident survivors.	radiation_sigs_morton_cossim
Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.	rcc_sig_activity
Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.	rcc_sim
Single Base Substitution COSMIC mutational signatures for 2780 tumors	sbs_palette
Single base substitution signature attributions found in Lung cancer in never smokers.	Sherlock_LCINS_SBS
Reference COSMIC Single base substitution signatures found in Lung cancer in never smokers.	Sherlock_LCINS_SBS.refs
Metadata accompanying mutational signatures for lung cancer in never smokers.	Sherlock_LCINS.metadata
Statistically compare the within-sample diversity and across-sample heterogeneity of the mutational signature activity in two or more groups of tumor samples.	sigboot
Compute the within-sample diversity and across-sample heterogeneity of mutational signature activity in one or multiple populations of samples.	sigvar
Activity of Smoking, APOBEC, and Ageing mutational signatures in a sample of East Asian lung adenocarcinoma patients.	smoker_sigs_chen
Cosine similarity of smoking, APOBEC, and ageing mutational signatures found in a sample of East Asian lung adenocarcinoma patients.	smoker_sigs_chen_cossim
Compute a normalized weighting vector based on a vector of sampling times.	time_weights
Counts of each context class for the main transcript of gene TP53	TP53_context_counts_ordered
Driver mutations from the intogen website for gene TP53 in lung adenocarcinomas	TP53_drivers_intogen_LUAD
SBS96 spectrum from the intogen website for gene TP53 in lung adenocarcinomas	TP53_drivers_intogen_SBS96
Activity of SBS mutational signatures in samples of lung cancer in never smokers	zhang_sig_activity
Cosine similarity of SBS mutational signatures found in samples of lung cancer in never smokers	zhang_sig_similarity