Package: splitTypeR 0.99.9

Astrid Deschênes

splitTypeR: Transcriptomic Classification using Mixture of Normal Distributions

The splitTypeR package enables the classification of bulk transcriptomic samples using gene signature lists. For each signature, an enrichment score is first calculated for every sample with Bioconductor GSVA, and the uncertainty around each score is estimated through permutations of the samples. Values drawn from the sample-specific normal distributions are then pooled to fit a mixture of two normal distributions that represents the whole cohort. Each sample is finally tested against the distribution with the lower mean, and samples with a significantly higher score are assigned to the signature. Published gene signatures related to pancreatic ductal adenocarcinoma subtyping are also provided.

Authors:Astrid Deschênes [aut, cre], Pascal Belleau [aut], David A. Tuveson [aut], Lustgarten Foundation [fnd]

splitTypeR_0.99.9.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
splitTypeR/json (API)

# Install 'splitTypeR' in R:

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

Bug tracker:https://github.com/adeschen/splittyper/issues

Datasets:

expNormalCountsDemo - Simulated normalized expected counts for 30 demonstration samples
signaturesDemo - Demonstration gene signatures for PDAC subtyping

On CRAN:

biologicalquestion classification genesetenrichment software

3.85 score 25 exports 129 dependencies

Last updated from:f19ea104fd. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	198
linux-devel	NOTE	651
source / vignettes	OK	573
linux-release	NOTE	637
macos-release	NOTE	499
macos-oldrel	NOTE	361
windows-devel	NOTE	577
windows-release	NOTE	593
windows-oldrel	NOTE	578
wasm-release	OK	164

Exports:classification classification<-getGeneSignatures getGeneSignaturesNames getGenesInSignature gsvaResults gsvaResults<-model model<-permutations permutations<-plotDensityWithUpscalingSamplesBimodal plotPermutationSamplesDistribution plotPermutationSamplesNormal runSubtypingBimodal show signatures signatures<-SplitTypeRdata standardDeviation standardDeviation<-threshold threshold<-upscaling upscaling<-

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocParallel Biostrings bit bit64 blob bslib cachem cli codetools cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue graph GSEABase GSVA gtable h5mread HDF5Array highr htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite KEGGREST kernlab knitr labeling lambda.r later lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mime mixtools nlme openssl otel pillar pkgconfig plotly png promises purrr R6 rappdirs RColorBrewer Rcpp rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales segmented Seqinfo SingleCellExperiment snow SparseArray sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable XVector yaml

Transcriptomic Classification using Mixture of Normal Distributions

Rendered fromsplitTypeR.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-02-28

Help page	Topics
Transcriptomic classification using multimodal distributions	splitTypeR-package splitTypeR
Generic function for getting the classification slot in a class	classification
Getter for the classification slot in a SplitTypeRdata class	classification,SplitTypeRdata-method
Generic function for replacement of the classification slot in a class	classification<-
Replacement of the classification slot in a 'SplitTypeRdata' object	classification<-,SplitTypeRdata-method
Simulated normalized expected counts for 30 demonstration samples	expNormalCountsDemo
Return the selected gene list signatures	getGeneSignatures
List the names of the available signatures	getGeneSignaturesNames
Return the genes for a specific signature	getGenesInSignature
Generic function for getting the gsvaResults slot in a class	gsvaResults
Getter for the signatures slot in a SplitTypeRdata class	gsvaResults,SplitTypeRdata-method
Generic function for replacement of gsvaResults slot in a class	gsvaResults<-
Replacement of gsvaResults slot in a 'SplitTypeRdata' object	gsvaResults<-,SplitTypeRdata-method
Class Union for list or NULL	ListOrNULL-class
Class Union for matrix or NULL	MatrixOrNULL-class
Generic function for getting the model slot in a class	model
Getter for the model slot in a SplitTypeRdata class	model,SplitTypeRdata-method
Generic function for replacement of model slot in a class	model<-
Replacement of model slot in a 'SplitTypeRdata' object	model<-,SplitTypeRdata-method
Generic function for getting the permutations slot in a class	permutations
Getter for the signatures slot in a SplitTypeRdata class	permutations,SplitTypeRdata-method
Generic function for replacement of permutations slot in a class	permutations<-
Replacement of permutations slot in a 'SplitTypeRdata' object	permutations<-,SplitTypeRdata-method
Graph both the alternative and the signature distributions obtained for a specific signature	plotDensityWithUpscalingSamplesBimodal
Graph showing both the alternative and the signature distributions obtained for a specific signature	plotPermutationSamplesDistribution
Graph the enrichment results as violin plots from the permutation step	plotPermutationSamplesNormal
Classification of heterogeneous biological samples based on gene signature lists using a mixture of two normal distributions	runSubtypingBimodal
Show a summary of a SplitTypeRdata object	show,SplitTypeRdata-method
Generic function for getting the signatures slot in a class	signatures
Getter for the signatures slot in a SplitTypeRdata class	signatures,SplitTypeRdata-method
Generic function for replacement of signatures slot in a class	signatures<-
Replacement of signatures slot in a 'SplitTypeRdata' object	signatures<-,SplitTypeRdata-method
Demonstration gene signatures for PDAC subtyping	signaturesDemo
Create a SplitTypeRdata object	SplitTypeRdata
An S4 class to represent the splitTypeR data	SplitTypeRdata-class
Generic function for getting the standardDeviation slot in a class	standardDeviation
Getter for the standardDeviation slot in a SplitTypeRdata class	standardDeviation,SplitTypeRdata-method
Generic function for replacement of standardDeviation slot in a class	standardDeviation<-
Replacement of the standardDeviation slot in a 'SplitTypeRdata' object	standardDeviation<-,SplitTypeRdata-method
Generic function for getting the threshold slot in a class	threshold
Getter for the threshold slot in a SplitTypeRdata class	threshold,SplitTypeRdata-method
Generic function for replacement of threshold slot in a class	threshold<-
Replacement of threshold slot in a 'SplitTypeRdata' object	threshold<-,SplitTypeRdata-method
Generic function for getting the upscaling slot in a class	upscaling
Getter for the upscaling slot in a SplitTypeRdata class	upscaling,SplitTypeRdata-method
Generic function for replacement of the upscaling slot in a class	upscaling<-
Replacement of the upscaling slot in a 'SplitTypeRdata' object	upscaling<-,SplitTypeRdata-method

Package: splitTypeR 0.99.9

splitTypeR: Transcriptomic Classification using Mixture of Normal Distributions

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