This package provides a package containing an environment representing the HG-U133B.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 HT\_HG-U133B\_probe\_tab.

This package provides a package containing an environment representing the HG-U133A_tag.CDF file.

This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".

Affymetrix hugene21 annotation data (chip hugene21stprobeset) assembled using data from public repositories.

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

Sample dataset obtained from http://www.hapmap.org.

Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories.

This package provides a package containing an environment representing the HG_U95D.CDF file.

This package provides a function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

An interactive tool to visualize long vectors of integer data by means of Hilbert curves.

This package provides a package containing an environment representing the Hu35KsubD.CDF file.

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

Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

Data used by the barcode package for microarrays of type hgu133a.

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 Hu35KsubC\_probe\_tab.

This package provides a package containing an environment representing the Hu6800subB.CDF file.

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

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-U219\_probe\_tab.

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

This package provides a package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177.

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.