User: Philip Lijnzaad

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Posts by Philip Lijnzaad

<prev • 30 results • page 1 of 3 • next >
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Comment: C: search @ support.bioconductor.org does not work on post titles. (Try e.g. search
... 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 16 days ago by Philip Lijnzaad • 160
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search @ support.bioconductor.org does not work on post titles. (Try e.g. searching ronaldfisher to find this very post back)
... 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 ...
bioconductor website support written 16 days ago by Philip Lijnzaad • 160
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DNABarcodes: finding length of barcode
... 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 ...
single-cell sequencing barcodes written 18 days ago by Philip Lijnzaad • 160
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DNABarcodes: issue with wrong barcode decoding
... 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 ...
single-cell sequencing barcodes written 18 days ago by Philip Lijnzaad • 160
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Comment: C: topGO crashes with ' argument "annotationFun" is missing, with no default'
... 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 2.5 years ago by Philip Lijnzaad • 160
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topGO crashes with ' argument "annotationFun" is missing, with no default'
... 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 ...
topgo bug written 2.5 years ago by Philip Lijnzaad • 160 • updated 2.5 years ago by James W. MacDonald ♦ 50k
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Comment: C: class "AsIs" is not valid for @'dataset' in an object of class "Mart"; is(value
... brilliant, thanks!   ...
written 2.5 years ago by Philip Lijnzaad • 160
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class "AsIs" is not valid for @'dataset' in an object of class "Mart"; is(value, "character")
... 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 == " ...
biomart bug written 2.5 years ago by Philip Lijnzaad • 160
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Comment: C: apply over the 'rows' of a GRanges object (and/or: is there a fiveprime() funct
... 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 2.7 years ago by Philip Lijnzaad • 160
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Comment: C: apply over the 'rows' of a GRanges object (and/or: is there a fiveprime() funct
... 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 2.7 years ago by Philip Lijnzaad • 160

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
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