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# Annotation Mus musculus
require(AnnotationHub)
ah <- AnnotationHub()
names(ah)[1:10]
ah <- query(ah, 'Mus musculus')
ah <- query(ah, 'Homo sapiens')
table(ah$dataprovider)
# UCSC
ucsc <- ah[ah$dataprovider=='UCSC'] # UCSC
table(ucsc$rdataclass) #-----
granges <- query(ucsc, 'GRanges') # 173 GRanges with UCSC tracks
table(granges$sourcetype)
txdbs <- query(ucsc, 'TxDb') # 5 TxDb G/T/P models
table(txdbs) # mm9/10
twobitfiles <- query(ucsc, 'twoBitFile') # 4 TwoBitFiles seqs
twobitfiles # mm7, 8, 9, 10
# NCBI # NCBI
ncbi <- query(ah, 'NCBI') #-----
# 1 org.Mm.eg.db with gene annotations
# Ensembl
ensembl <- ah[ah$dataprovider == 'Ensembl']
table(ensembl$rdataclass) # Ensembl
#---------
ensdbs <- query(ensembl, 'EnsDb') # 12 EnsDb: 87->98
ensdbs$title
twobitfiles <- query(ensembl, 'twoBitFile') # 815 TwoBitFile seqs
sort(table(twobitfiles$genome), decreasing=TRUE)
twobitfiles <- query(twobitfiles,'GRCm38') # 75 GRCm38 (others: BALB_cJ_v1, C3H_HeJ_v1, ...)
data.frame(names(twobitfiles)[order(twobitfiles$title)], twobitfiles$title[order(twobitfiles$title)])
twobitfiles['AH49772'] # Lots of data redundancy due to periodic automated builds
twobitfiles['AH50117'] # https://support.bioconductor.org/p/125690
table(twobitfiles$title) # cdna, dna(_r|sm), ncrna
granges <- query(ensembl, 'GRanges') # 556 GRanges GTFs
granges[1]
sort(granges$title)
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