Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,538 results • page 2 of 154 • next >
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Comment: C: CDS phase information missing from GenomicFeatures
... OK. So we could add a warning in makeTxDbFromGFF() when the phases reported in the file for the CDS in a transcript don't agree with the phases inferred from the CDS cumwidths. Not a totally satisfying solution because only the person who calls makeTxDbFromGFF() to create the TxDb object gets to se ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: CDS phase information missing from GenomicFeatures
... To add some historic background here: TxDb objects were originally designed to support correct gene models from UCSC and Ensembl (via makeTxDbFromUCSC and makeTxDbFromEnsembl). So at the time it didn't feel necessary to include the phase information. Note that the UCSC tracks don't contain this inf ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: CDS phase information missing from GenomicFeatures
... Hi, To me this only reveals that the CDS reported in example.gff is incorrect. Why would the CDS be reported to start at position 1 if the start codon for transcript g1.t1 is at position 2-4? In other words, shouldn't the phase of the 1st CDS in a transcript always be 0? H. ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: GenomicAlignments - extracting sequence signatures from bam file
... Hi, If your FASTA file contains a single sequence (which should be the case if it's HIV reference genome) then everything is going to be much easier if you load it as Michael suggested i.e. with genome <- read.DNAStringSet()[[1]]. Then genome will be a DNAString object instead of a DNAStringSet ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: BiocGenerics built with R 3.4.2 changes behaviour
... There is a regression in R 3.4.2 that affects S4 generics with dispatch on the ellipsis. The bug is in the methods package and breaks code like sapply(x, paste, collapse="") (where x is a list of character vectors) by not passing the collapse argument to the internal calls to paste(). We've implemen ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: BiocGenerics built with R 3.4.2 changes behaviour
... Hi, After installing R 3.4.2 I was able to reproduce this. The upgrade to R 3.4.2 also caused many other failures in many other Bioconductor packages. We advice users to NOT upgrade their installation to R 3.4.2 while we investigate this. Cheers, H. ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Implementing fast mathematical and statistical operations on genomic variables i
... I'm not sure yet. We'll need to come up with a plan to make the transition as smooth as possible. But we are not here yet. H. ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Plans for multicore block processing in DelayedArray?
... The plan for RleArray and RleMatrix objects is to use a seed (RleArraySeed) that supports chunking. This will allow better compression and more efficient block processing (especially in the case of multicore block processing) than a DataFrame of Rle's wrapped in a DelayedArray. Furthermore, this ch ...
written 8 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Plans for multicore block processing in DelayedArray?
... I expect multicore block processing to improve speed but how much exactly will depend on the type of DelayedArray object. Let's keep in mind that with on-disk DelayedArray objects (HDF5Array), the cores will compete for I/O. And it's not clear to me that N cores trying to read N HDF5 blocks concurre ...
written 8 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Plans for multicore block processing in DelayedArray?
... The timeline is: as soon as possible! I'll do my very best to have this into the next BioC release. Cheers. H. ...
written 8 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 5 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 5 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 6 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 6 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 6 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 7 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 7 months ago, voted at least 25 times.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 7 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Commentator 7 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 9 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 9 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 19 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 19 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 19 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 19 months ago, created an answer that has been accepted. For A: how much positions overlapped for each pair of the pairs obtained by findover
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

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