Package: SigsPack 1.21.0

Franziska Schumann

SigsPack: Mutational Signature Estimation for Single Samples

Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.

Authors:Franziska Schumann <[email protected]>

SigsPack_1.21.0.tar.gz
SigsPack_1.21.0.zip(r-4.5)SigsPack_1.21.0.zip(r-4.4)SigsPack_1.21.0.zip(r-4.3)
SigsPack_1.21.0.tgz(r-4.4-any)SigsPack_1.21.0.tgz(r-4.3-any)
SigsPack_1.21.0.tar.gz(r-4.5-noble)SigsPack_1.21.0.tar.gz(r-4.4-noble)
SigsPack_1.21.0.tgz(r-4.4-emscripten)SigsPack_1.21.0.tgz(r-4.3-emscripten)
SigsPack.pdf |SigsPack.html✨
SigsPack/json (API)
NEWS

# Install 'SigsPack' in R:

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

Bug tracker:https://github.com/bihealth/sigspack/issues

Datasets:

cosmicSigs - COSMIC Signature Profiles
hg19context_freq - Trinuecleotide frequencies of the human reference genome hg19
sigProfiler20190522 - COSMIC v3 whole genome SBS Signature Profiles
sigProfilerExome - COSMIC v3 exome SBS Signature Profiles

On BioConductor:SigsPack-1.21.0(bioc 3.21)SigsPack-1.20.0(bioc 3.20)

somaticmutation snp variantannotation biomedicalinformatics dnaseq

4.30 score 2 stars 4 scripts 163 downloads 1 mentions 9 exports 71 dependencies

Last updated 23 days agofrom:7943dfb283. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:bootstrap_mut_catalogues create_mut_catalogues decomposeQP get_context_freq normalize plot_bootstrapped_exposure signature_exposure summarize_exposures vcf2mut_cat

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png quadprog R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml zlibbioc

Introduction to SigsPack

Rendered fromSigsPack.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-08-15
Started: 2019-04-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bootstraps a given mutational catalogue	bootstrap_mut_catalogues
COSMIC Signature Profiles	cosmicSigs
Creates simulated mutational catalogues	create_mut_catalogues
decomposeQP function	decomposeQP
Extract occurence of tri-nucleotide contexts	get_context_freq
Trinuecleotide frequencies of the human reference genome hg19	hg19context_freq
Normalize mutational catalogues	normalize
Plot signature exposure estimation for several samples	plot_bootstrapped_exposure
Estimates the signature exposure of a mutational catalogue	signature_exposure
COSMIC v3 whole genome SBS Signature Profiles	sigProfiler20190522
COSMIC v3 exome SBS Signature Profiles	sigProfilerExome
Signature exposure analysis of a mutational catalogue	summarize_exposures
Derive the mutational catalogue from a vcf	vcf2mut_cat