Package: signeR 2.9.0

Renan Valieris

signeR: Empirical Bayesian approach to mutational signature discovery

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Authors:Rafael Rosales, Rodrigo Drummond, Renan Valieris, Alexandre Defelicibus, Israel Tojal da Silva

signeR_2.9.0.tar.gz
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signeR.pdf |signeR.html✨
signeR/json (API)
NEWS

# Install 'signeR' in R:

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

Bug tracker:https://github.com/tojallab/signer/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

cosmic_data - COSMIC Mutational Signatures
tcga_similarities - TCGA Cosmic similarities
tcga_tumors - TCGA tumors used on TCGA Explorer

On BioConductor:signeR-2.9.0(bioc 3.21)signeR-2.8.0(bioc 3.20)

genomicvariation somaticmutation statisticalmethod visualization bioconductor bioinformatics

7.67 score 13 stars 22 scripts 216 downloads 9 mentions 31 exports 232 dependencies

Last updated 19 days agofrom:1531a164ee. Checks:OK: 1 WARNING: 6 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 08 2024
R-4.5-win-x86_64	WARNING	Nov 08 2024
R-4.5-linux-x86_64	WARNING	Nov 08 2024
R-4.4-win-x86_64	WARNING	Nov 08 2024
R-4.4-mac-x86_64	WARNING	Nov 08 2024
R-4.4-mac-aarch64	NOTE	Nov 08 2024
R-4.3-win-x86_64	WARNING	Nov 08 2024
R-4.3-mac-x86_64	WARNING	Nov 08 2024
R-4.3-mac-aarch64	NOTE	Nov 08 2024

Exports:Average_exp Average_sign BICboxplot DiffExp ExposureBarplot ExposureBoxplot ExposureClassify ExposureClassifyCV ExposureCorrelation ExposureGLM ExposureHeat ExposureSurvival ExposureSurvModel FuzzyClustExp genCountMatrixFromMAF genCountMatrixFromVcf genOpportunityFromGenome HClustExp Median_exp Median_sign Normalize Paths Reorder_mutations Reorder_samples Reorder_signatures setMutations setSamples signeR signeRFlow SignHeat SignPlot

Dependencies:abind ada AnnotationDbi askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob boot broom BSgenome bslib bsplus BWStest cachem car carData class cli clipr clue cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray Deriv digest doBy doParallel dplyr DT e1071 evaluate exactRankTests extrafont extrafontdb fansi farver fastmap filelock fontawesome forcats foreach formatR Formula fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glmnet globals glue gmp gridBase gridExtra gridtext gtable highr hms htmltools htmlwidgets httpuv httr igraph inaparc IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST kknn km.ci KMsurv knitr kpeaks kSamples labeling lambda.r later lattice lazyeval lhs lifecycle listenv lme4 lubridate magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv microbenchmark mime minqa modelr multcompView munsell mvtnorm nlme nloptr NMF nnet numDeriv openssl parallelly pbkrtest pheatmap pillar pkgconfig plogr plyr PMCMRplus png polynom ppclust prettyunits pROC progress promises proxy purrr pvclust quantreg R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr registry reshape2 restfulr Rhtslib rjson rlang rmarkdown Rmpfr rngtools rpart Rsamtools RSQLite rstatix rtracklayer Rttf2pt1 S4Arrays S4Vectors sass scales shape shiny shinycssloaders shinydashboard shinyWidgets snow sourcetools SparseArray SparseM stringi stringr SummarizedExperiment SuppDists survival survivalAnalysis survminer survMisc sys tibble tidyr tidyselect tidytidbits timechange tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs VGAM viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

signeR

Rendered fromsigneR-vignette.Rhtmlusingknitr::knitron Nov 08 2024.

Last update: 2023-10-18
Started: 2016-09-12

signeRFlow

Alexandre Defelicibus

Rendered fromsigneRFlow.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2023-10-16
Started: 2022-07-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Empirical Bayesian approach to mutational signature discovery	signeR-package
COSMIC Mutational Signatures	cosmic_data
Differential Exposure Analysis	DiffExp DiffExp,SignExp,character-method
Classify samples by exposure levels	ExposureClassify ExposureClassify,ANY,character-method ExposureClassify,SignExp,character-method
k-fold cross-validation of sample classifcation by exposure levels	ExposureClassifyCV ExposureClassifyCV,ANY,character-method ExposureClassifyCV,SignExp,character-method
Exposure correlation analysis (given a known sample feature)	ExposureCorrelation ExposureCorrelation,matrix,numeric-method ExposureCorrelation,SignExp,numeric-method
Exposure Generalized Linear Model	ExposureGLM ExposureGLM,matrix,numeric-method ExposureGLM,SignExp,numeric-method
Exposure survival analysis	ExposureSurvival ExposureSurvival,matrix,character-method ExposureSurvival,matrix,Surv-method ExposureSurvival,matrix-method ExposureSurvival,SignExp,character-method ExposureSurvival,SignExp,Surv-method ExposureSurvival,SignExp-method
Exposure Cox model	ExposureSurvModel ExposureSurvModel,matrix,character-method ExposureSurvModel,matrix,Surv-method ExposureSurvModel,matrix-method ExposureSurvModel,SignExp,character-method ExposureSurvModel,SignExp,Surv-method ExposureSurvModel,SignExp-method
Fuzzy Clustering of exposure data	FuzzyClustExp FuzzyClustExp,SignExp,numeric-method FuzzyClustExp,SignExp-method
count matrix and opportunity matrix generators	genCountMatrixFromMAF genCountMatrixFromVcf genOpportunityFromGenome
Hierarchical Clustering of exposure data	HClustExp HClustExp,SignExp,numeric-method HClustExp,SignExp-method
SignExp class methods	Average_exp Average_exp,SignExp-method Average_sign Average_sign,SignExp-method Median_exp Median_exp,SignExp-method Median_sign Median_sign,SignExp-method Normalize Normalize,SignExp-method Reorder_mutations Reorder_mutations,SignExp,numeric-method Reorder_samples Reorder_samples,SignExp,numeric-method Reorder_signatures Reorder_signatures,SignExp,numeric-method setMutations setMutations,SignExp-method setSamples setSamples,SignExp-method
signeR plot functions	BICboxplot ExposureBarplot ExposureBarplot,SignExp-method ExposureBoxplot ExposureBoxplot,SignExp-method ExposureHeat ExposureHeat,SignExp-method Paths Paths,SignExp-method SignHeat SignHeat,SignExp-method SignPlot SignPlot,SignExp-method
signeR	signeR
Launch signeRFlow R Shiny web app	signeRFlow
SignExp class	SignExp SignExp-class
TCGA Cosmic similarities	tcga_similarities
TCGA tumors used on TCGA Explorer	tcga_tumors