User: Aditya

gravatar for Aditya
Aditya120
Reputation:
120
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Trusted
Location:
Germany
Last seen:
1 day, 6 hours ago
Joined:
4 years, 5 months ago
Email:
a*************@mpi-bn.mpg.de

Posts by Aditya

<prev • 67 results • page 1 of 7 • next >
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Comment: C: Are AH52264, AH66175, and AH70594 duplicates?
... Thank you Lori :-) . ...
written 1 day ago by Aditya120
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Are AH52264, AH66175, and AH70594 duplicates?
... 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 ...
annotationhub written 1 day ago by Aditya120 • updated 1 day ago by shepherl ♦♦ 1.6k
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... Aha, so that's the new paradigm - thx - will use that! ...
written 2 days ago by Aditya120
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 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 Aditya120
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... Owkies, clear now, thx Martin! ...
written 3 days ago by Aditya120
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 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 Aditya120
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 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 Aditya120
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Annotating GRanges with TxDb gene models using plyranges
... 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 ...
plyranges written 3 days ago by Aditya120
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 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 Aditya120
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TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 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 ...
txdb.hsapiens.ucsc.hg38.knowngene txdb.mmusculus.ucsc.mm10.ensgene written 4 days ago by Aditya120 • updated 4 days ago by James W. MacDonald51k

Latest awards to Aditya

Student 13 months ago, asked a question with at least 3 up-votes. For Best way to convert uniprot accessions to entrez gene identifiers in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Error: hgu95av2PFAM is defunct
Supporter 13 months ago, voted at least 25 times.
Great Question 13 months ago, created a question with more than 5,000 views. For Best way to convert uniprot accessions to entrez gene identifiers in R
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Best way to convert uniprot accessions to entrez gene identifiers in R
Scholar 4.2 years ago, created an answer that has been accepted. For A: DAVIDWebService$new(): Error: .jinit(...) == 0 is not TRUE
Scholar 4.5 years ago, created an answer that has been accepted. For A: DAVIDWebService$new(): Error: .jinit(...) == 0 is not TRUE

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