User: Aditya

gravatar for Aditya
Aditya • 70
Reputation:
70
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Trusted
Location:
Germany
Last seen:
23 hours ago
Joined:
4 years, 3 months ago
Email:
a*************@mpi-bn.mpg.de

Posts by Aditya

<prev • 26 results • page 1 of 3 • next >
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Is mm10.p6 available as BSgenome?
... [BSgenome.Mmusculus.UCSC.mm10][2] contains mm10 ([2012 version][1]). Is [mm10.patch 6 - 2017][3]: also available as a BSgenome? [1]: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ [2]: https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm10.html [ ...
bsgenome.mmusculus.ucsc.mm10 written 2 days ago by Aditya • 70 • updated 19 hours ago by James W. MacDonald ♦ 50k
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vcountPDict: full versus masked BSgenome
... Is vcountPDict identical when performed against full or masked BSgenome? Any performance benefit for masked BSgenome? Small example below suggests it doesn't matter, is that conclusion generalizable? # Function to count genome matches count_genome_matches <- function(cas9seqs, bsgen ...
bsgenome biostrings bsgenome.mmusculus.ucsc.mm10::mmusculus written 4 days ago by Aditya • 70
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Comment: C: vcountPDict fails on PDict
... Oh, thank you Herve :-) ...
written 7 days ago by Aditya • 70
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Comment: C: getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
... This works, but relies on using (BioC non-complyingly) non-exported functionality - can this be done better? bsname <- BSgenome:::.getInstalledPkgnameFromProviderVersion('mm10') bsgenome <- utils::getFromNamespace(bsname, bsname) ...
written 7 days ago by Aditya • 70
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getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)
... Is there a way to avoid BiocGenerics, S4Vectors, IRanges, and Biostrings from being attached when calling BSgenome::getBSgenome() ? bsgenome <- BSgenome::getBSgenome('mm10') Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: c ...
bsgenome bsgenome.mmusculus.ucsc.mm10 written 7 days ago by Aditya • 70
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Comment: C: How to subset a BSgenome
... Thank you Lori :-) . ...
written 14 days ago by Aditya • 70
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vcountPDict fails on PDict
... # vcountPDict on a DNAStringSet works bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus seqs <- c("CTTATATTGTCTCCAGCAGAAGG", "CTTATATTGTCTCCAGCAGAAGG", "ATATTGTCAAGTTGACAACCAGG") Biostrings::vcountPDict( Biostrings::DNAStringSet(seqs), bsgenome, min.m ...
biostrings written 15 days ago by Aditya • 70 • updated 7 days ago by Hervé Pagès ♦♦ 14k
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How to subset a BSgenome
... # Load a BSgenome object bs <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus # Extracting a single chromosome works fine bs[['chr1']] bs[['chr2']] # Question: how to take a BSgenome subset? bs[c('chr1', 'chr2')] Error in bsgenome[c("chr1", "chr2")] : object of type 'S ...
bsgenome bsgenome.mmusculus.ucsc.mm10 written 15 days ago by Aditya • 70 • updated 15 days ago by shepherl ♦♦ 1.4k
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Comment: C: Biostrings regex matching
... Thank you Herve :-). ...
written 10 weeks ago by Aditya • 70
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Biostrings regex matching
... How to do Biostrings regex matching? chr1 <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus$chr1 Biostrings::countPattern('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA', chr1) [1] 363 Biostrings::countPattern('A{44}', chr1, fixed = FALSE) Error in .Call2("new_XString_from_ ...
biostrings written 11 weeks ago by Aditya • 70 • updated 10 weeks ago by Hervé Pagès ♦♦ 14k

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Student 11 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 11 months ago, created a question with more than 1,000 views. For Error: hgu95av2PFAM is defunct
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Great Question 11 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 3.3 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 4.1 years ago, created an answer that has been accepted. For A: DAVIDWebService$new(): Error: .jinit(...) == 0 is not TRUE
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