Admin: Hervé Pagès

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Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès

<prev • 1,449 results • page 1 of 145 • next >
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Answer: A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
... Hi Sophie, An important thing to keep in mind is that trying to access the internals of an S4 object with @ is almost always a bad idea. In Bioconductor, all S4 objects should be accessed/manipulated via accessor functions or other functions or methods. In the case of DNAStringSet objects, the only ...
written 1 day ago by Hervé Pagès ♦♦ 12k
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Comment: C: Multiple Sequence Alignment using DNA sequence
... Hi, This is an interesting problem. I'm curious to hear from Erik Wright, the author of the DECIPHER package, about this. IIRC Erik is doing something like this in DECIPHER to efficiently align/compare DNA sequences. The "reverse-translation" step is clearly the challenge here, given that the mappi ...
written 1 day ago by Hervé Pagès ♦♦ 12k
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Answer: A: intersect ranges from a GAlignment object with a GRangesList
... Hi Carlos, I would suggest you check coverageByTranscript in the GenomicFeatures package. It will compute the per-transcript (or per-CDS) coverage of your set of reads. Once you have this for your set of CDS (say in cds_cvg, will be an RleList object with 1 integer-Rle per CDS), you can easily get ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: I'm developing a package. How can I specify a dependent package to be installed
... The xlsxjars Windows and Mac binaries provided on CRAN should work. If they don't, then that's probably something that you'd want to discuss with the xlsxjars maintainers and/or the CRAN folks. It's good that you found a workaround that fixes the problem for you but that doesn't really address the i ...
written 7 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: I'm developing a package. How can I specify a dependent package to be installed
... Hi, Note that questions about package development should be asked on the bioc-devel mailing list. Not sure why you'd want to take control over the installation options of a dependent package. Doesn't sound like a good idea to me. Note that these options are only relevant when installing from sourc ...
written 7 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Cannot Install BSgenome.Hsapiens.UCSC.hg19
... Yep, I recognize this warning: Warning in file.append(to[okay], from[okay]):   write error during file append I had it once while I was trying to install a big package (was not a BSgenome data package), and, after scratching my head for a while, it turned out that I had consumed my disk quota ...
written 7 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: Cannot Install BSgenome.Hsapiens.UCSC.hg19
... Hi, The BSgenome packages depend on rtracklayer and the rtracklayer Mac binary that we distribute as part of BioC 3.5 is currently broken. You should be able to reproduce the above error by just trying to load rtracklayer with library(rtracklayer). This is a known issue and we are working on it. Se ...
written 8 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: NGS with summarizeOverlaps and SAM files
... Note that this isn't a GenomicRanges question either. The summarizeOverlaps() function is defined in the GenomicAlignments package. summarizeOverlaps() uses scanBam() from the Rsamtools package behind the scene to load the aligned reads. Calling scanBam() on a SAM file wrapped in a BamFile object is ...
written 8 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: check splice isoforms
... Maybe it would help people on this forum help you if you could provide a little bit more details e.g. what's in your FASTQ files. H. ...
written 9 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: binnedaverage - is it possible to add an na.rm option?
... Hi Janet, A very reasonable request. I just added this to GenomicRanges 1.28.2 (BioC release) and 1.29.4 (BioC devel). Please allow between 24 and 48 hours for these new versions to become available via biocLite(). Cheers, H. PS: Nice to see you back here! ...
written 9 days ago by Hervé Pagès ♦♦ 12k

Latest awards to Hervé Pagès

Scholar 6 days ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 10 days ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 15 days ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 20 days ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 27 days ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 28 days ago, voted at least 25 times.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 5 weeks ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 3 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 3 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 13 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 13 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 13 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 13 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 13 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Scholar 13 months ago, created an answer that has been accepted. For A: Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Scholar 13 months ago, created an answer that has been accepted. For A: resize (shrink/expand) GenomicRanges
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?

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