User: Aditya
Aditya • 120
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Posts by Aditya
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3
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... Are `AH52264`, `AH66175` and `AH70594` duplicates, arisen due to automated snapshotting of the same resource at different dates?
ah <- AnnotationHub() # all
ucsc <- query(ah, 'UCSC') # ucsc
txdbs <- query(ucsc, 'TxDb') # txdb
txdbs
title ...
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... Aha, so that's the new paradigm - thx - will use that! ...
written 2 days ago by
Aditya • 120
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... It makes dependency management a bit trickier, though, since a Hub resource cannot be imported in a package (can it?). The price to pay for the increased volumes and sizes of data? Or has a new workflow paradigm superseeded the need for data packages alltogether? ...
written 3 days ago by
Aditya • 120
0
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172
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... Owkies, clear now, thx Martin! ...
written 3 days ago by
Aditya • 120
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... Thankyou James.
I was wondering about the design concept as to what is packaged and what is hubbed.
I notice, e.g. that the UCSC TxDbs are packaged, whereas the Ensembl EnsDbs are hubbed.
From this I can infer two alternative design rules, and I am wondering which one is correct:
1. BioC packag ...
written 3 days ago by
Aditya • 120
0
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... Two separate questions
1. I've noticed that BioC is moving away from annnotation packages (old style) to the AnnotationHub interface (new style). Is anyone willing to comment on this evolution?
2. UCSC uses the NCBI gene models, right (or does it have its own, third set, besides Ensembl and NCBI?) ...
written 3 days ago by
Aditya • 120
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... I have two GRanges objects: (1) TFBS and (2) GENEMODELS
# (1) TFBS: Transcription factor binding sites (for SRF)
bedfile <- paste0('https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis',
'/uploads/a51e98516c1e6b71441f5b5a5f741fa1/SRF.bed')
TFB ...
written 3 days ago by
Aditya • 120
0
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1
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172
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... Thank you James - very enlightening!
I found an alternative in `GenomicFeatures::makeTxDbFromEnsembl(organism = 'Homo sapiens')`, but that doesn't get the seqinfo right (I wonder why):
txdb <- GenomicFeatures::makeTxDbFromEnsembl(organism = 'Homo sapiens')
GenomeInfoDb::seqinfo(txdb)
...
written 3 days ago by
Aditya • 120
2
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1
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... For **mouse**, BioC offers both entrezg- and ensembl-centric TxDbs:
# Entrezg
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
GenomicFeatures::genes(txdb)[c('100009600', '99889', '99982')]
# Ensembl
txdb <- Tx ...
written 4 days ago by
Aditya • 120
• updated
4 days ago by
James W. MacDonald ♦ 51k
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For Error: hgu95av2PFAM is defunct
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For A: DAVIDWebService$new(): Error: .jinit(...) == 0 is not TRUE
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