XAItest
This is the released version of XAItest; for the devel version, see XAItest.
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]
, Sébastien HERGALANT [aut]
Maintainer: Ghislain FIEVET <ghislain.fievet at gmail.com>
citation("XAItest")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/XAItest/ |
| Package Short Url | https://bioconductor.org/packages/XAItest/ |
| Package Downloads Report | Download Stats |