Package: supersigs 1.20.0

Albert Kuo

supersigs: Supervised mutational signatures

Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

Authors:Albert Kuo [aut, cre], Yifan Zhang [aut], Bahman Afsari [aut], Cristian Tomasetti [aut]

supersigs_1.20.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
supersigs/json (API)

# Install 'supersigs' in R:

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

Bug tracker:https://github.com/tomasettilab/supersigs/issues

Pkgdown/docs site:https://tomasettilab.github.io

Datasets:

example_dt - Example dataset of mutations
supersig_ls - Trained SuperSigs from TCGA

On CRAN:

featureextraction classification regression sequencing wholegenome somaticmutation

2.95 score 3 stars 5 scripts 384 downloads 6 exports 94 dependencies

Last updated from:589553e6b3 (on RELEASE_3_23). Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	307
linux-devel	ERROR	466
source / vignettes	ERROR	363
linux-release	ERROR	409
macos-release	ERROR	276
macos-oldrel	ERROR	302
windows-devel	ERROR	378
windows-release	ERROR	360
windows-oldrel	ERROR	329
wasm-release	OK	264

Exports:get_signature make_matrix partial_signature predict_signature process_vcf simplify_signature

Dependencies:abind assertthat Biobase BiocGenerics Biostrings caret class cli clock codetools cpp11 crayon data.table DelayedArray diagram digest dplyr e1071 farver foreach furrr future future.apply generics GenomicRanges ggplot2 globals glue gower gtable hardhat ipred IRanges isoband iterators KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix MatrixGenerics matrixStats ModelMetrics nlme nnet numDeriv parallelly pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp recipes reshape2 rlang rpart rsample S4Arrays S4Vectors S7 scales Seqinfo shape slider SparseArray sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite warp withr XVector

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example dataset of mutations	example_dt
Function to obtain a SuperSig	get_signature
Function to transform mutations into "matrix" format	make_matrix
Function to remove the contribution of a SuperSig	partial_signature
Function to predict using SuperSig object	predict_signature
Function to transform VCF object into "matrix" format	process_vcf
Function to simplify signature representation into interpretable labels for visualization purposes	simplify_signature
Trained SuperSigs from TCGA	supersig_ls
An S4 class for SuperSig	SuperSig SuperSig-class