Cross-hybridisation study on the ATH1 Affymetrix GeneChip.

xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_laevis\_2\_probe\_tab.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Xenopus\_laevis\_probe\_tab.

Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).

Multi-level model for cross-study detection of differential gene expression.

xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.

Base annotation databases for xenopus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include parquet', h5', and mtx files. The package mainly represents data as SpatialExperiment objects.

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_tropicalis\_probe\_tab.

This package provides data to use with xcore package.

This package provides a package containing an environment representing the Xenopus_laevis.cdf file.

This package provides a package containing an environment representing the X_laevis_2.CDF file.

This package provides a package containing an environment representing the X_tropicalis.cdf file.

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.

This package provides a package containing an environment representing the Ye6100subD.CDF file.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was YG-S98\_probe\_tab.

This package provides a collection of different sets of experimental data from yeast.

This package provides a package containing an environment representing the Ye6100subB.CDF file.

This package provides a selection of RNA-Seq data from a yeast transcriptome experiment.

This package provides a collection of so-called gold (and other) standard data sets.

ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment.