Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories.

Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) assembled using data from public repositories.

Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories.

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

This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).

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.

An R Package for Geneset Enrichment Workflows.

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

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

Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories.

HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

This package provides tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel.

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

Affymetrix Affymetrix HG_U95B Array annotation data (chip hgu95b) assembled using data from public repositories.

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.

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

Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) 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.

HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.

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\_MG-430B\_probe\_tab.

This package provides a package containing an environment representing the HG_U95B.CDF file.

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

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.