This is an ExperimentHub Data package that helps to access the spatially-resolved transcriptomics and single-nucleus RNA sequencing data. The datasets are generated from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. The datasets are based on [spatial_hpc](https://github.com/LieberInstitute/spatial_hpc) project by Lieber Institute for Brain Development (LIBD) researchers and collaborators.

This package provides a package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.

Annotation data file for humanCHRLOC assembled using data from public data 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 HT\_MG-430B\_probe\_tab.

Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

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

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

This package provides a package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.

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

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 Hu35KsubC.CDF file.

This package was created by frmaTools version 1.9.2.

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

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.

Package with metadata for genotyping Illumina 650k arrays using the crlmm package.

An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.

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

Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories.

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

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 HC-G110\_probe\_tab.

Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) assembled using data from public repositories.

Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) 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 HT\_HG-U133B\_probe\_tab.