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 HT\_Rat-Focus\_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 HG-U133A\_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 Hu35KsubA\_probe\_tab.

Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) assembled using data from public repositories.

hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Package with metadata for genotyping Illumina 550k arrays using the crlmm package.

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

This package provides a package containing an environment representing the Hu6800.CDF file.

This package was created by frmaTools version 1.13.0.

R objects describing the HEEBO oligo set.

Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional.

Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) assembled using data from public repositories.

This package contains the data used in the vignettes and examples of the h5vc package.

Package with metadata for genotyping Illumina 660kQuad arrays using the crlmm package.

The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.

Affymetrix huex10 annotation data (chip huex10stprobeset) assembled using data from public repositories.

This package provides a package containing an environment representing the HT_HG-U133_Plus_PM.CDF file.

Package with metadata fast genotyping Illumina 1M arrays using the crlmm package.

FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) assembled using data from public repositories.

Package with metadata for genotyping Illumina Omni2.5 Quad arrays using the crlmm package.

This package provides a package containing an environment representing the HG_U95C.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 Hu35KsubB\_probe\_tab.

Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) assembled using data from public repositories.