Package: STATegRa 1.43.0

David Gomez-Cabrero

STATegRa: Classes and methods for multi-omics data integration

Classes and tools for multi-omics data integration.

Authors:STATegra Consortia

STATegRa_1.43.0.tar.gz
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STATegRa.pdf |STATegRa.html✨
STATegRa/json (API)
NEWS

# Install 'STATegRa' in R:

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

Datasets:

Block1 - STATegRa data
Block1.PCA - STATegRa data
Block2 - STATegRa data
Block2.PCA - STATegRa data
TCGA_BRCA_Data - STATegRa data
ed - STATegRa data
ed.PCA - STATegRa data
mapdata - STATegRa data

On BioConductor:STATegRa-1.43.0(bioc 3.21)STATegRa-1.42.0(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

4.15 score 3 scripts 220 downloads 7 mentions 22 exports 50 dependencies

Last updated 23 days agofrom:7a5e8cca09. Checks:OK: 1 NOTE: 6. Indexed: yes.

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

Exports:bioDist bioDistclass bioDistFeature bioDistFeaturePlot bioDistW bioDistWPlot bioMap combiningMappings createOmicsExpressionSet getInitialData getLoadings getMethodInfo getPreprocessing getScores getVAF holistOmics modelSelection omicsCompAnalysis omicsNPC plotRes plotVAF STATegRaUsersGuide

Dependencies:affy affyio Biobase BiocGenerics BiocManager bitops calibrate caTools cli codetools colorspace edgeR fansi farver foreach generics ggplot2 glue gplots gridExtra gtable gtools isoband iterators KernSmooth labeling lattice lifecycle limma locfit magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig preprocessCore R6 RColorBrewer rlang scales statmod tibble utf8 vctrs viridisLite withr zlibbioc

STATegRa User's Guide

The STATegra Consortium

Rendered fromSTATegRa.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2018-04-24
Started: 2014-10-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
bioDist	bioDist bioDist,character,character,bioMap,ExpressionSet,ExpressionSet-method
bioDistclass	bioDistclass
bioDistFeature	bioDistFeature bioDistFeature,character,list,numeric-method
bioDistFeaturePlot	bioDistFeaturePlot
bioDistW	bioDistW bioDistW,character,list,matrix-method
bioDistWPlot	bioDistWPlot bioDistWPlot,character,list,character-method
bioMap	bioMap
caClass	caClass-class
combiningMappings, combining several mappings for use in the omicsNPC function	combiningMappings
createOmicsExpressionSet	createOmicsExpressionSet createOmicsExpressionSet,matrix-method
Retrieve initial data from caClass objects	getInitialData getInitialData,caClass-method
Retrieve component analysis loadings	getLoadings getLoadings,caClass-method
Retrieve information about component analysis method	getMethodInfo getMethodInfo,caClass-method
Retrieve information about preprocessing	getPreprocessing getPreprocessing,caClass-method
Retrieve component analysis scores	getScores getScores,caClass-method
Retrieve information abotut VAF	getVAF getVAF,caClass-method
HolistOmics an application of NPC on omics datasets	holistOmics holistOmics,list,character-method
Find optimal common and distinctive components	modelSelection modelSelection,list,numeric,character-method
Components analysis for multiple objects	omicsCompAnalysis omicsCompAnalysis,list,character,character,numeric,numeric-method
omicsNPC, applying the Non-Parametric Combination (NPC) on omics datasets	omicsNPC omicsNPC,list,data.frame-method omicsNPC,list,missing-method
Plot component analysis results	plotRes plotRes,caClass,numeric,character,character,logical-method
Plot VAF (Variance Explained For) from Component Analysis	plotVAF plotVAF,caClass-method
STATegRa	STATegRa-package STATegRa
STATegRa data	Block1 Block1.PCA Block2 Block2.PCA ed ed.PCA mapdata STATegRa_data
STATegRa data	STATegRa_data_TCGA_BRCA TCGA_BRCA_Data
Defunct functions in STATegRa	STATegRa-defunct
STATegRaUsersGuide	STATegRaUsersGuide