XAItest

This is the released version of XAItest; for the devel version, see XAItest.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

XAItest: Enhancing Feature Discovery with eXplainable AI

Bioconductor version: Release (3.23)

XAItest is an R Package that identifies features using eXplainable AI (XAI) methods such as SHAP or LIME. This package allows users to compare these methods with traditional statistical tests like t-tests, empirical Bayes, and Fisher's test. Additionally, it includes simThresh, a system that enables the comparison of feature importance with p-values by incorporating calibrated simulated data.

Author: Ghislain FIEVET [aut, cre] ORCID: 0000-0002-0337-7327 , Sébastien HERGALANT [aut] ORCID: 0000-0001-8456-7992

Maintainer: Ghislain FIEVET <ghislain.fievet at gmail.com>

Citation (from within R, enter citation("XAItest")):

Ghislain FIEVET, Sébastien HERGALANT. XAItest: XAItest: Enhancing Feature Discovery with eXplainable AI. doi:10.18129/B9.bioc.XAItest, R package version 1.4.0, https://bioconductor.org/packages/XAItest.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("XAItest")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("XAItest")

01_XAItest	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, FeatureExtraction, Regression, Software, StatisticalMethod
Version	1.4.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0)
Imports	limma, randomForest, kernelshap, caret, lime, DT, methods, SummarizedExperiment, ggplot2
System Requirements
URL	https://github.com/GhislainFievet/XAItest
Bug Reports	https://github.com/GhislainFievet/XAItest/issues

Suggests	knitr, ggforce, shapr (>= 1.0.1), airway, xgboost, BiocGenerics, RUnit, S4Vectors
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	XAItest_1.4.0.tar.gz
Windows Binary (x86_64)	XAItest_1.3.2.zip
macOS Binary (big-sur-x86_64)	XAItest_1.4.0.tgz
macOS Binary (sonoma-arm64)	XAItest_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/XAItest
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/XAItest
Package Short Url	https://bioconductor.org/packages/XAItest/
Package Downloads Report	Download Stats