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 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-430\_PM\_probe\_tab.

HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.

This package provides a package containing an environment representing the Hu35KsubA.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 Hu35KsubD\_probe\_tab.

agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories.

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

Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories.

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

This package was automatically created by package AnnotationDbi version 1.11.8. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg19.

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 Hu6800\_probe\_tab.

Affymetrix hugene10 annotation data (chip hugene10stprobeset) assembled using data from public repositories.

Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) assembled using data from public repositories.

This package was created by frmaTools version 1.13.0.

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 Hu35KsubA Array annotation data (chip hu35ksuba) 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.

hammers is a utilities suite for scRNA-seq data analysis compatible with both Seurat and SingleCellExperiment. It provides simple tools to address tasks such as retrieving aggregate gene statistics, finding and removing rare genes, performing representation analysis, computing the center of mass for the expression of a gene of interest in low-dimensional space, and calculating silhouette and cluster-normalized silhouette.

The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie.

Annotation data file for humanCHRLOC assembled using data from public data repositories.

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

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.

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.

Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) assembled using data from public repositories.