Package with metadata for genotyping Illumina Omni1 Quad arrays using the crlmm package.

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

Agilent Human 1A (V2) annotation data (chip hgug4110b) assembled using data from public repositories.

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\_tag\_probe\_tab.

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

Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) assembled using data from public repositories.

This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories.

This package provides a package containing an environment representing the HG-U133B.cdf file.

HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6.

This package provides a package containing an environment representing the Hu6800subC.CDF file.

This package provides a package containing an environment representing the Hu35KsubC.CDF file.

This package provides a package containing an environment representing the Hu35KsubB.CDF file.

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

This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881.".

This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

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

This package provides a package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.

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-U95B\_probe\_tab.

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

This package provides a package containing an environment representing the HG-U133A_2.cdf file.

Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories.

Data used by the barcode package for microarrays of type hgu133plus2.