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.

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 HuGene-1\_0-st-v1\_probe\_tab.

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

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

Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) assembled using data from public repositories.

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

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

The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data.

Package with metadata for genotyping Illumina 370kQuad arrays using the crlmm package.

This package provides a package containing an environment representing the HG-U133_Plus_2.cdf file.

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

Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories.

This package provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and DESeq2` as well as voom differential expression analyses are available.

Package with metadata for genotyping Illumina 610kQuad 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 HG-Focus\_probe\_tab.

Unknown annotation data (chip hgubeta7) assembled using data from public repositories.

This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

This package provides a package containing an environment representing the HG-U133A.cdf file.

agilent AMADID 026652 annotation data (chip hgug4845a) 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.

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

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

This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.