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Genome wide annotation for Human: Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.
Full genomic sequences for Homo sapiens (UCSC genome hg38): Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are stored in DNAString objects.
Genome wide annotation for Mouse: Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers.
A set of annotation maps describing the entire Gene Ontology: A set of annotation maps describing the entire Gene Ontology assembled using data from GO
Annotation package for TxDb object(s): Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6): Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, based on GRCm38.p6) and stored in Biostrings objects.
Annotation package for TxDb object(s): Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
SNP locations for Homo sapiens (dbSNP Build 144): SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
Annotation package for TxDb object(s): Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
Platform Design Info for Affymetrix HuGene-1_0-st-v1: Platform Design Info for Affymetrix HuGene-1_0-st-v1
Ensembl based annotation package: Exposes an annotation databases generated from Ensembl.
Annotation package for Illumina Infinium DNA methylation probes: Compiled HumanMethylation27 and HumanMethylation450 annotations
Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13): Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects.
Species and taxonomy ID look up tables used by GenomeInfoDb: Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.
Annotation package for the Homo.sapiens object: Contains the Homo.sapiens object to access data from several related annotation packages.
Ensembl based annotation package: Exposes an annotation databases generated from Ensembl.
Annotation package for TxDb object(s): Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
Ensembl based annotation package: Exposes an annotation databases generated from Ensembl.
Genome wide annotation for Fly: Genome wide annotation for Fly, primarily based on mapping using Entrez Gene identifiers.
Full genome sequences for Homo sapiens (GRCh38): Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.
Full genome sequences for Mus musculus (UCSC version mm9): Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.
Illumina HumanHT12v3 annotation data (chip illuminaHumanv3): Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) assembled using data from public repositories
An alignment of molecular sequences, structures or profiles derived from them.
Affymetrix Human Genome 219 Plate annotation data (chip hgu219): Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories
bovinecdf: A package containing an environment representing the Bovine.cdf file.
Full genome sequences for Bos taurus (UCSC version bosTau4): Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.
EnsDbs for AnnotationHub: 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.
Full genome sequences for Arabidopsis thaliana (TAIR9): 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 masked genome sequences for Bos taurus (UCSC version bosTau3): Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
Full genome sequences for Arabidopsis thaliana (TAIR version from April 23, 2008): Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.
Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1): Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.
Full genome sequences for Apis mellifera (Amel_HAv3.1): Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects.
Full genome sequences for Bos taurus (UCSC version bosTau3): Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.
agcdf: A package containing an environment representing the AG.CDF file.
Full masked genome sequences for Apis mellifera (UCSC version apiMel2): Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.
Affymetrix Affymetrix AG Array annotation data (chip ag): Affymetrix Affymetrix AG Array annotation data (chip ag) assembled using data from public repositories
SQLites, tibbles, and data.tables for AnnotationHub: Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow](https://github.com/rikenbit/pubmed-workflow). For the details, see the README.md of pubmed-workflow.
Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501): Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501) assembled using data from public repositories
Full genome sequences for Canis lupus familiaris (UCSC version canFam2): Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.
high resolution naturalearth data for rnaturalearth
Affymetrix Affymetrix Bovine Array annotation data (chip bovine): Affymetrix Affymetrix Bovine Array annotation data (chip bovine) assembled using data from public repositories
Alternative splicing event annotation for Human (hg38): 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.
CytoBands for AnnotationHub: Supplies AnnotationHub with CytoBand information from UCSC. There is a track for each major organism. Giemsa-stained bands are commonly used to decorate chromosomal overviews in visualizations of genomic data.
Metabolites and proteins linked to PathBank pathways (for AnnotationHub): The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis.
Metabolites linked to WikiPathways pathways (for AnnotationHub): The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.
barley1cdf: A package containing an environment representing the Barley1.CDF file.
One or more molecular sequences, possibly with associated annotation.|This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
Probe sequence data for microarrays of type bovine: 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 Bovine\_probe\_tab.