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Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,609 results • page 1 of 161 • next >
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Comment: C: GenomeInfoDb's Seqinfo() error on hg38
... Should be fixed in GenomeInfoDb 1.19.2 (devel, see commit [here]( https://github.com/Bioconductor/GenomeInfoDb/commit/18c1056adb2304b0e194df31acbf061c6f6ec04b)) and 1.18.2 (release). These new versions won't show up on the build reports ([devel](https://bioconductor.org/checkResults/devel/bioc-LATES ...
written 11 days ago by Hervé Pagès ♦♦ 13k
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Answer: A: GenomeInfoDb's Seqinfo() error on hg38
... Hi Mike, Sequences like `chr15_KN538374v1_fix` don't belong to GRCh38 but to recent patched versions of GRCh38 (e.g. GRCh38.p12, which is the latest). Unfortunately it looks like the UCSC folks updated the `chromInfo` table for hg38 a couple of days ago, and that the table now contains chrom info f ...
written 11 days ago by Hervé Pagès ♦♦ 13k
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Answer: A: error in makeTxDbFromUCSC
... Thanks for the report. The refGene tables in UCSC databases hg19 and hg38 were last updated in Nov 2018 and now contain transcripts located on sequences that do NOT belong to the corresponding genomes (GRCh37 and GRCh38, respectively). More precisely some transcripts in these tables now belong to * ...
written 26 days ago by Hervé Pagès ♦♦ 13k
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Answer: A: Using non standard charachters with XStrings object in BioStrings
... Hi, Main problem with those codes is that they are not 1-letter codes so wouldn't play well with the "1 letter per nucleotide" paradigm that is at the core of nucleotide sequence representation in Biostrings. So the 1st thing I would recommend is to use 1-letter codes to represent those exotic nucl ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: DataFrame matrix subsetting
... Hi Felix, My guess is that the `[` method for DataFrame objects doesn't know how to handle a logical matrix subscript in a way that mimics what happens with ordinary data frames or matrices. Note that in such case `df[m]` can simply be obtained with `as.matrix(df)[m]` so the workaround is pretty st ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Best way of creating a large RleMatrix
... The change to the constructor is that it now accepts a list-like object of Rle objects (e.g. RleList object or DataFrame of Rle's). Each list element in this list-like object becomes a chunk. So yes, if the input to the constructor is a DataFrame of Rle's then each column of the DataFrame becomes a ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Best way of creating a large RleMatrix
... Hi, Sorry for the late answer. I've been doing some work on the RleArray() constructor to improve support for long RleArray/RleMatrix objects. One of them is that calling the RleArray() constructor directly on a DataFrame with Rle columns now is supported and fast. I've also added plenty of example ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Biostrings install error
... Hi, Are you using BiocManager::install() as recommended to install and update packages? It will spare you version mismatch headaches like the above. H. ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Biostrings - translate gives wrong results for triplets TTG and CTG
... This has been discussed and addressed on GitHub: https://github.com/Bioconductor/Biostrings/issues/15 H. ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Modify Biostrings script
... You'll have to try it. Also make sure to set no.init.codon to TRUE when calling translate() on sequences where the initiation codon has been removed or truncated. no.init.codon is a new argument to translate():   https://github.com/Bioconductor/Biostrings/commit/dcd915c21b96d4d981d4530f913ff910823 ...
written 3 months ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 6 weeks ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: how to extract "Gene type" from org.Mm.eg.db?
Popular Question 5 months ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Popular Question 5 months ago, created a question with more than 1,000 views. For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Scholar 5 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Popular Question 5 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Scholar 5 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 8 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 8 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 9 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: extract subsequence(s) from DNAStringSet with getSeq
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: about setdiff() and meta-information in GRanges
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Error when running "locateVariants" function in "VariantAnnotation" package
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 20 months ago, created an answer with at least 3 up-votes. For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Error in GRanges: could not find symbol "recursive" in environment of the generi

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