Package: ClustAll 1.3.0

Asier Ortega-Legarreta

ClustAll: ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types).

Authors:Asier Ortega-Legarreta [aut, cre], Sara Palomino-Echeverria [aut]

ClustAll_1.3.0.tar.gz
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ClustAll_1.3.0.tgz(r-4.4-any)ClustAll_1.3.0.tgz(r-4.3-any)
ClustAll_1.3.0.tar.gz(r-4.5-noble)ClustAll_1.3.0.tar.gz(r-4.4-noble)
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ClustAll.pdf |ClustAll.html✨
ClustAll/json (API)
NEWS

# Install 'ClustAll' in R:

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

Datasets:

heart_data - Heart Disease Dataset
obj_noNA1 - Obj_noNA1: Processed wdbc dataset for testing purposed
obj_noNA1simplify - Obj_noNA1simplify: Processed wdbc dataset for testing purposed
obj_noNAno1Validation - Obj_noNAno1Validation: Processed wdbc dataset for testing purposed
wdbc - Wdbc: Diagnostic Wisconsin Breast Cancer Database.
wdbcMIDS - WdbcMIDS: Diagnostic Wisconsin Breast Cancer Database with imputed values
wdbcNA - WdbcNA: Diagnostic Wisconsin Breast Cancer Database with missing values

On BioConductor:ClustAll-1.3.0(bioc 3.21)ClustAll-1.2.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software statisticalmethod clustering dimensionreduction principalcomponent

4.00 score 1 scripts 184 downloads 19 exports 172 dependencies

Last updated 2 months agofrom:3058c84135. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	OK	Dec 19 2024
R-4.5-linux	OK	Dec 19 2024
R-4.4-win	OK	Dec 19 2024
R-4.4-mac	OK	Dec 19 2024
R-4.3-win	OK	Dec 19 2024
R-4.3-mac	OK	Dec 19 2024

Exports:addValidationData cluster2data createClustAll dataImputed dataOriginal dataValidation extractData extractResults JACCARD_DISTANCE_F nImputation plotJACCARD plotSANKEY processed resStratification runClustAll show showData summary_clusters validateStratification

Dependencies:abind backports base64enc bigassertr bigparallelr bigstatsr BiocGenerics bit bit64 boot broom bslib cachem car carData circlize class cli clipr clue cluster clValid codetools colorspace ComplexHeatmap cowplot cpp11 crayon crosstalk DEoptimR Deriv digest diptest doBy doParallel doSNOW dplyr DT ellipse emmeans estimability evaluate FactoMineR fansi farver fastmap fBasics ff flashClust flexmix flock fontawesome forcats foreach Formula fpc fs generics GetoptLong ggplot2 ggrepel glmnet GlobalOptions glue gss gtable haven highr hms htmltools htmlwidgets httpuv igraph IRanges isoband iterators jomo jquerylib jsonlite kernlab knitr labeling later lattice lazyeval leaps lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats mclust memoise mgcv mice microbenchmark mime minqa mitml modeest modelr modeltools multcompView munsell mvtnorm networkD3 nlme nloptr nnet numDeriv ordinal pan parallelly pbapply pbkrtest pillar pkgconfig png prabclus prettyunits progress promises ps purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr RhpcBLASctl rjson rlang rmarkdown rmio rmutil robustbase rpart RSpectra S4Vectors sass scales scatterplot3d shape snow SparseM spatial stable stabledist statip stringi stringr survival tibble tidyr tidyselect timeDate timeSeries tinytex tzdb ucminf utf8 vctrs viridisLite vroom withr xfun yaml

ClustAll User's Guide

Asier Ortega-Legarreta and Sara Palomino-Echeverria

Rendered fromVignette_Clustall.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-09-22
Started: 2023-11-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add Validation Data to ClustAllObject	addValidationData addValidationData,ClustAllObject,numericOrCharacter-method
Class Union: characterOrNA	characterOrNA-class
ClustAllObject	ClustAllObject-class
Export Stratification Results with Original Data	cluster2data cluster2data,ClustAllObject,character-method
Create ClustAllObject for Patient Stratification Analysis	createClustAll createClustAll,data.frame,numericOrNA,ANY,characterOrNA-method
Retrieve Imputed Data from ClustAllObject	dataImputed dataImputed,ClustAllObject-method
Retrieve Original Unprocessed Data from ClustAllObject	dataOriginal dataOriginal,ClustAllObject-method
Retrieve Validation Data from ClustAllObject	dataValidation dataValidation,ClustAllObject-method
extractData	extractData extractData,ClustAllObject-method
Extract Clustering Results from ClustAllObject	extractResults extractResults,ClustAllObject-method
Heart Disease Dataset	heart_data
initializeClustAllObject	initialize,ClustAllObject-method
Retrieve Jaccard Distance Matrix for Robust Stratifications	JACCARD_DISTANCE_F JACCARD_DISTANCE_F,ClustAllObject-method
Class Union: listOrNULL	listOrNULL-class
Class Union: logicalOrNA	logicalOrNA-class
Class Union: matrixOrNULL	matrixOrNULL-class
Retrieve Number of Imputations from ClustAllObject	nImputation nImputation,ClustAllObject-method
Class Union: numericOrCharacter	numericOrCharacter numericOrCharacter-class
Class Union: numericOrNA	numericOrNA-class
obj_noNA1: Processed wdbc dataset for testing purposed	obj_noNA1
obj_noNA1simplify: Processed wdbc dataset for testing purposed	obj_noNA1simplify
obj_noNAno1Validation: Processed wdbc dataset for testing purposed	obj_noNAno1Validation
Visualize Jaccard Distances Between Robust Stratifications	plotJACCARD plotJACCARD,ClustAllObject,logicalOrNA,numericOrNA-method
Visualize Stratification Comparisons with Sankey Diagram	plotSANKEY plotSANKEY,ClustAllObject,character,logicalOrNA-method
Check Processing Status of ClustAllObject	processed processed,ClustAllObject-method
Extract Representative Stratifications from ClustAllObject	resStratification resStratification,ClustAllObject,numericOrNA,logicalOrNA,numericOrNA-method
Execute ClustALL Algorithm on a ClustAllObject	runClustAll runClustAll,ClustAllObject,numericOrNA,logicalOrNA-method
Display Summary of ClustAllObject	show,ClustAllObject-method
Retrieve Processed Data from ClustAllObject	showData showData,ClustAllObject-method
Retrieve Summary of Clustering Results from ClustAllObject	summary_clusters summary_clusters,ClustAllObject-method
Validate Stratification Results Against True Labels	validateStratification validateStratification,ClustAllObject,characterOrNA-method
wdbc: Diagnostic Wisconsin Breast Cancer Database.	wdbc
wdbcMIDS: Diagnostic Wisconsin Breast Cancer Database with imputed values	wdbcMIDS
wdbcNA: Diagnostic Wisconsin Breast Cancer Database with missing values	wdbcNA