UCSC

bioinformatics
database
Published

September 24, 2024

Modified

October 14, 2024

UCSC

rtracklayer

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library(rtracklayer)
library(AnnotationHub)

# 第一次下载  ah <- AnnotationHub()
ah <- AnnotationHub()
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ah
AnnotationHub with 71634 records
# snapshotDate(): 2024-04-30
# $dataprovider: Ensembl, BroadInstitute, UCSC, ftp://ftp.ncbi.nlm.nih.gov/g...
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Rattus norv...
# $rdataclass: GRanges, TwoBitFile, BigWigFile, EnsDb, Rle, OrgDb, SQLiteFil...
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5012"]]' 

             title                                             
  AH5012   | Chromosome Band                                   
  AH5013   | STS Markers                                       
  AH5014   | FISH Clones                                       
  AH5015   | Recomb Rate                                       
  AH5016   | ENCODE Pilot                                      
  ...        ...                                               
  AH117051 | Ensembl 112 EnsDb for Xiphophorus maculatus       
  AH117052 | Ensembl 112 EnsDb for Xenopus tropicalis          
  AH117053 | Ensembl 112 EnsDb for Zonotrichia albicollis      
  AH117054 | Ensembl 112 EnsDb for Zalophus californianus      
  AH117055 | Ensembl 112 EnsDb for Zosterops lateralis melanops
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# C:/Users/DELL/AppData/Local/R/cache/R/AnnotationHub/
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OrgDb_Human <- subset(ah, rdataclass == "OrgDb" & species == "Homo sapiens")
OrgDb_Human
AnnotationHub with 1 record
# snapshotDate(): 2024-04-30
# names(): AH116710
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Homo sapiens
# $rdataclass: OrgDb
# $rdatadateadded: 2024-04-02
# $title: org.Hs.eg.db.sqlite
# $description: NCBI gene ID based annotations about Homo sapiens
# $taxonomyid: 9606
# $genome: NCBI genomes
# $sourcetype: NCBI/ensembl
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.ensembl.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH116710"]]'
Show the code
org <- OrgDb_Human[[1]]
org
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMAN_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| EGSOURCEDATE: 2024-Mar12
| EGSOURCENAME: Entrez Gene
| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| CENTRALID: EG
| TAXID: 9606
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: http://current.geneontology.org/ontology/go-basic.obo
| GOSOURCEDATE: 2024-01-17
| GOEGSOURCEDATE: 2024-Mar12
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| KEGGSOURCENAME: KEGG GENOME
| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
| KEGGSOURCEDATE: 2011-Mar15
| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
| GPSOURCEURL: 
| GPSOURCEDATE: 2024-Feb29
| ENSOURCEDATE: 2023-Nov22
| ENSOURCENAME: Ensembl
| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
| UPSOURCENAME: Uniprot
| UPSOURCEURL: http://www.UniProt.org/
| UPSOURCEDATE: Thu Apr 18 21:39:39 2024
Show the code
GRanges_Human <- subset(ah, rdataclass == "GRanges" & species == "Homo sapiens")

gr <- GRanges_Human[1]
gr
AnnotationHub with 1 record
# snapshotDate(): 2024-04-30
# names(): AH5012
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2013-03-26
# $title: Chromosome Band
# $description: GRanges object from UCSC track 'Chromosome Band'
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: UCSC track
# $sourceurl: rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/hg19/database...
# $sourcesize: NA
# $tags: c("cytoBand", "UCSC", "track", "Gene", "Transcript",
#   "Annotation") 
# retrieve record with 'object[["AH5012"]]'