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... I see that the biostars.org website has the same behaviour. So it is part of the original code base, which I suppose it is less easily fixed? Still, an unfortunate design decision to be able to search only the content of posts but not the titles. ...
written 5 months ago by Philip Lijnzaad160
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... Not sure this is the right place to ask, but right now the search box at the top of this very page does not work for words occurring in the titles of posts. To see what I mean, try searching for **ronaldfisher** which I deliberately included in the title of this post. It is reasonable to expect thi ...
written 5 months ago by Philip Lijnzaad160
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... Dear all, the demultiplex function in the very nice DNABarcodes package (Tilo Buschmann) returns a data.frame with, per read, the original read (including the original barcode); the decyphered (i.e. error-corrected) barcode, and the total edit distance between original barcode and error-corr ...
written 5 months ago by Philip Lijnzaad160
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... I'm a happy user of the DNABarcodes package by Tilo Buschmann. I came across the paper by Hawkins, John A., Stephen K. Jones, Ilya J. Finkelstein, and William H. Press. 2018. “Indel-Correcting DNA Barcodes for High-Throughput Sequencing.” Proceedings of the National Academy of Sciences 115 (27): E62 ...
written 5 months ago by Philip Lijnzaad160
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... grmpf, you are right, thank you! (would have been nice if one were warned with an 'unused argument' here ... ). It turns out that I had another mistake (made by trying out all the possible combinations of possibilities), it must be annot = annFUN.org, rather than annot = annFUN.db. It would be nic ...
written 2.9 years ago by Philip Lijnzaad160
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... What am I doing wrong here?  I scoured the (incomplete and confusing) documentation, but I get stuck at the 'new' function/method (which is not documented), which says Building most specific GOs ..... Error in .local(.Object, ...) :   argument "annotationFun" is missing, with no default Yet I am c ...
written 2.9 years ago by Philip Lijnzaad160 • updated 2.9 years ago by James W. MacDonald51k
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... brilliant, thanks!   ...
written 2.9 years ago by Philip Lijnzaad160
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... Given the following: library(biomaRt) mart <- useMart("ensembl") list <- listDatasets(m) dataset.name <- list[ grep("sapiens",list\$dataset, ignore.case=TRUE), 'dataset' ] list clearly shows a data.frame containing character strings, is.character( dataset.name) is TRUE, dataset.name == " ...
written 2.9 years ago by Philip Lijnzaad160
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... You are right, I missed that, silly. I maintain though that it is wrong to have "start" sometimes mean "leftmost coordinate regardless of strand", and sometimes "5'-coordinate", even for objects that have a strand ... it confuses the hell out of biologists who occasionally use these data types.  Wo ...
written 3.1 years ago by Philip Lijnzaad160
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... Thanks for your quick answer > We can do that with resize(gr, 1) That is cool and very concise, but nearly everywhere in the documentation "start" means: leftmost coordinate, not 5'-coordinate of the feature at hand. E.g. start(GRanges(IRanges(start=10, end=20), strand='-', seqnames="x")) yi ...
written 3.1 years ago by Philip Lijnzaad160