Package: IWTomics 1.37.0

Marzia A Cremona

IWTomics: Interval-Wise Testing for Omics Data

Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

Authors:Marzia A Cremona, Alessia Pini, Francesca Chiaromonte, Simone Vantini

IWTomics_1.37.0.tar.gz
IWTomics_1.37.0.zip(r-4.7)IWTomics_1.37.0.zip(r-4.6)IWTomics_1.37.0.zip(r-4.5)
IWTomics_1.37.0.tgz(r-4.6-any)IWTomics_1.37.0.tgz(r-4.5-any)
IWTomics_1.37.0.tar.gz(r-4.7-any)IWTomics_1.37.0.tar.gz(r-4.6-any)
IWTomics_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IWTomics/json (API)

# Install 'IWTomics' in R:

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

Datasets:

ETn_example - ETn Recombination hotspots data
features_example - Example of features
regions_example - Example of regions
regionsFeatures_center - Example of '"IWTomicsData"' object with center alignment
regionsFeatures_scale - Example of '"IWTomicsData"' object with scale alignment

On BioConductor:IWTomics-1.37.0(bioc 3.24)IWTomics-1.36.0(bioc 3.23)

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

statisticalmethod multiplecomparison differentialexpression differentialmethylation differentialpeakcalling genomeannotation dataimport

3.48 score 6 scripts 1 mentions 26 exports 49 dependencies

Last updated from:a1b513d2ff. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	174
linux-devel-x86_64	WARNING	303
source / vignettes	OK	234
linux-release-x86_64	WARNING	266
macos-release-arm64	WARNING	146
macos-oldrel-arm64	WARNING	131
windows-devel	WARNING	207
windows-release	WARNING	202
windows-oldrel	WARNING	189
wasm-release	OK	142

Exports:adjusted_pval alignment features idFeatures idFeaturesTest idRegions idRegionsTest IWTomicsData IWTomicsTest lengthFeatures lengthRegions merge metadata nameFeatures nameRegions nFeatures nRegions nTests plot.IWTomicsData plotSummary plotTest regions resolution show smooth testInput

Dependencies:ash BiocGenerics bitops cli cluster colorspace cpp11 deSolve farver fda fds FNN generics GenomicRanges ggplot2 glue gtable hdrcde IRanges isoband kernlab KernSmooth ks labeling lattice lifecycle locfit MASS Matrix mclust mgcv multicool mvtnorm nlme pcaPP pracma R6 rainbow RColorBrewer Rcpp RCurl rlang S4Vectors S7 scales Seqinfo vctrs viridisLite withr

Introduction to IWTomics

Rendered fromIWTomics.Rnwusingknitr::knitr

Last update: 2018-09-07
Started: 2016-11-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Interval-Wise Testing for Omics Data	IWTomics-package IWTomics
ETn Recombination hotspots data	ETn_example
Example of features	features_example
Class '"IWTomicsData"'	adjusted_pval alignment c,IWTomicsData-method cbind,IWTomicsData-method features idFeatures idFeaturesTest idRegions idRegionsTest IWTomicsData IWTomicsData,character,character-method IWTomicsData,character,data.frame-method IWTomicsData,character,matrix-method IWTomicsData,GRangesList,list-method IWTomicsData-class lengthFeatures lengthRegions merge,IWTomicsData,IWTomicsData-method metadata nameFeatures nameRegions nFeatures nRegions nTests rbind,IWTomicsData-method regions resolution show,IWTomicsData-method testInput [,IWTomicsData,ANY,ANY,ANY-method
Interval-Wise Testing	IWTomicsTest
Plot '"IWTomicsData"' object	plot plot,IWTomicsData-method
Summary plots of Interval-Wise Testing result	plotSummary
Detailed plots of Interval-Wise Testing result	plotTest
Example of regions	regions_example
Example of '"IWTomicsData"' object with center alignment	regionsFeatures_center
Example of '"IWTomicsData"' object with scale alignment	regionsFeatures_scale
Smooth curves of a '"IWTomicsData"' object	smooth smooth,IWTomicsData-method