The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data.

The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included.

This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes.

This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.

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.

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.

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.

This package provides data to use with xcore package.

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).

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 Xenopus_laevis.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 X\_tropicalis\_probe\_tab.

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 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.

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

Affymetrix Xenopus laevis annotation data (chip xlaevis) assembled using data from public repositories.

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.

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.

Cross-hybridisation study on the ATH1 Affymetrix GeneChip.

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

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

The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation.

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.