Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

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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 4 weeks 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 5 weeks 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 5 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Modify Biostrings script
... Hi, There is no need to start translating from the conserved site at the 3' end to stay in frame. When a read is truncated at the 5' end, all you need to do is trim 1 or 2 nucleotides on its 5' end to be in frame again. Or maybe you don't need to trim anything if the truncation preserved the frame. ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Initial List of Deprecated Package Bioc 3.9
... Maybe we could start by having a BiocViews term that we use to identify this type of package. Although this would make them "findable" only if you search/browse the right BioC version because our view trees are version specific: https://bioconductor.org/packages/release/BiocViews.html#___Software P ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Pull out sequences between ranges?
... Hi, Are you sure myGRangesObject is a GRanges object and not a GRangesList object? Anyway you first need to come up with a GRanges (or GRangesList) object containing the genomic ranges of the sequences you want to pull out. For example, to grab the 1000 base pairs upstream of the ranges in myGRang ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... I might change a little bit the interface of the RleArray() constructor function though (e.g. replacing the chunksize argument with chunkdim). Other than that, as long as you don't serialize your RleMatrix instances and your code doesn't try to access directly the internals of these objects, any cha ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Doesn't that limit to the total size of the matrix since it spans all columns? Indeed. I should add that one of the original motivations for coming up with ChunkedRleArraySeed was exactly this limitation. I wanted to be able to load the 1.3 Million Brain Cell Dataset (https://bioconductor.org/packa ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Hi, The exact internal representation of an RleArray object is still a work-in-progress and subject to change. The 2 current *RleArraySeed classes reflect the 2 experimentations I did so far with this. ChunkedRleArraySeed came after SolidRleArraySeed and improves on it by replacing a single Rle by ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Indexing large chromosomes (like wheat) bam files in Rsamtools
... I agree with Mike that this doesn't look like an issue related to Rsamtools. Please understand that It is very hard for the people watching this support site to help you if they cannot reproduce the error you're getting. So it would be of great help if you could provide a self-contained example that ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Popular Question 12 weeks ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 12 weeks ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question 12 weeks ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 12 weeks ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Popular Question 12 weeks ago, created a question with more than 1,000 views. For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 6 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 6 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 6 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 7 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: extract subsequence(s) from DNAStringSet with getSeq
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: about setdiff() and meta-information in GRanges
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 17 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 17 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
Scholar 17 months ago, created an answer that has been accepted. For A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
Scholar 17 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Error when running "locateVariants" function in "VariantAnnotation" package
Scholar 17 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 17 months ago, created an answer that has been accepted. For A: extract subsequence(s) from DNAStringSet with getSeq

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