Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.

Data needed by the affycomp package.

Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories.

Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the ensembldb package employing the Ensembl Perl API.

This package contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.

Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.

Six arrays. Three from amplified RNA, three from the typical procedure.

Full genomic sequences for UCSC genome hs1 (the hs1 genome is based on assembly T2T-CHM13v2.0, with GenBank assembly accession GCA_009914755.4). The sequences are stored in DNAString objects.

Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm10, based on GRCm38.p6) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal6, Mar. 2018) and stored in Biostrings objects.

Parse GFF and GTF files using C++ classes. The package also provides utilities to read and write GFF3 files. The GFF (General Feature Format) format is a tab-delimited file format for describing genes and other features of DNA, RNA, and protein sequences. GFF files are often used to describe the features of genomes.

Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome.

Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet.

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

An small dataset that can be used to run examples from the beadarray vignette and examples.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.

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 Bsubtilis\_probe\_tab.

This package provides tools to normalize (several) Hi-C data from replicates.

Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.

This package provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.