Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,602 results • page 2 of 161 • next >
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Comment: C: BSgenome package building
... Yep. And don't fix the DESCRIPTION file. Fix the seed file instead and re-generate the package with forgeBSgenomeDataPkg("path/to/my/seed"). Also show us your seed file if things are still not working. Thanks! ...
written 8 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: makeTxDbFromGFF errors too many NAs and make.splicings
... Hi Karl, The issue with the 1st file (Trinity_kmer10.gff3.gz) is that it contains start/end values greater than 2^31-1. The problem was that, because these values cannot be stored in an R integer vector, makeTxDbFromGFF() was silently coercing them to NAs. I committed a change to rtracklayer (versi ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: converting a fasta file to .2bit format
... Hi, Some very basic programming concepts are the notion of value, class, and variable. A call like Biostrings::readDNAStringSet("wheatreference.fasta") returns a value (in this particular case the value is a DNAStringSet instance i.e. an object of class DNAStringSet). If you don't store this value ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Calling coverage on GRanges object yields small negative values
... round(cov) with some number of digits is a good option. FWIW cov[cov < 0] <- 0 is slow because of the way x[i] <- value is currently implemented on Rle objects. The [<- method for Rle objects needs to be optimized. However, note that in the particular case of  cov[cov < 0] <- 0, a ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Build GPos from IPos
... This is another reasonable feature request. Also added to the TODO list: https://github.com/Bioconductor/GenomicRanges/issues/13 Thanks, H. ...
written 10 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Intra-range transformation on GPos-objects?
... Most of these transformations could indeed be supported on GPos objects. The intra-range transformations (shift, narrow, resize, flank, promoters, reflect, restrict, and trim) are generally expected to behave like endomorphisms (i.e. return an object of the same class as the input) so we would need ...
written 10 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: ChIPQC: error during annotation compilation
... Hi Thomas, Please note that GRanges objects were never intended to support unlist(). However it used to be that unlist() would work on them, just by chance, and be a no-op. Not sure why your code calls unlist() on a GRanges object or what you expected it to do. What has changed in BioC 3.7 is that ...
written 12 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: GenomicAlignments: Inverting strand when counting using summarizeOverlaps
... Hi Patrick, It depends on the stranded protocol that was used to generate your paired-end RNA-seq data. But first (and before I get to the details): Since I posted my original answer to this thread 3.5 years ago, 3 important functionalities have been added to the GenomicAlignments package: GAli ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Extracting fasta sequences from a RE digested genome .bed file
... Hi, Load the genomic coordinates of your fragments with rtracklayer::import(), use the object returned by rtracklayer::import() to extract the corresponding DNA sequences from the BSgenome object for mm9, then write the sequences to a FASTA file with Biostrings::writeXStringSet(). Will look somethi ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: subsetByOverlaps : comparing GRANGES and keeping all the information in the MET
... So how would you like the output to look like? Can you forge the output "by hand" (for input gr2 and gr1) and show it here so I can see/understand what you would expect this enhanced subsetByOverlaps() to return? Note that GRanges objects are not particularly good/convenient for representing one-to ...
written 3 months ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Popular Question 11 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 11 weeks ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 11 weeks ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question 11 weeks ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 11 weeks ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Popular Question 11 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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