Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

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Comment: C: Future plans for the new GPos class
... No plans to support this in the immediate future. I'm putting this on the TODO list and will get to it after the BioC 3.7 release (scheduled for May 1st). In the mean time, you can work around this by coercing to GRanges first. I recognize that this defeats the purpose of using a GPos object in the ...
written 13 days ago by Hervé Pagès ♦♦ 13k
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Comment: C: Extract genomic features from a TxDb-like object
... It's a DNAStringSetList object, not a DNAStringSet object. A DNAStringSetList object is a list-like object where each list element is a DNAStringSet object. Like with an ordinary list, you can extract individual list elements of a DNAStringSetList object with [[ or unlist the object with unlist(). B ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Extract genomic features from a TxDb-like object
... Hi, Let's separate the 2 issues you seem to be having: (1) the use of different chromosome naming conventions for Athaliana between plantsmart28 and UCSC, and (2) getPromoterSeq() failing to extract out-of-bounds ranges. Issue (1) can be addressed by setting the same sequence style on the 2 object ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: converting ensembl transcript ID to ensemble gene: problem & missing values
... Please ask this as a new question. Thanks! ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: extracting promoter sequences
... Thx! Now I see the output of sessionInfo() but I don't see a question. The title of your post is "extracting promoter sequences" which gives us a hint of what you're trying to do but you still need to formulate a question somewhere in your post. ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: extracting promoter sequences
... Do you realize that your post is almost impossible to read? ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
... This is actually a new question so it should be asked as such. This way people can find it when they search our support site. The GenomeInfoDb package provides no specific tools for retrieving the assembly gaps. If your assembly is supported by the UCSC Genome Browser, then just import the "gap" ta ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
... Hi Nathan, Have you tried si <- Seqinfo(genome="canFam3"); seqlengths(si) ? It supports many of the most commonly used UCSC assemblies. See ?Seqinfo in the GenomeInfoDb package for more information (don't miss the examples). Let me know if your assembly is not supported and we'll add it. Cheers ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: In GenomicRanges, how to narrow down search of duplicated names in case of "'seq
... Hi, You need to look for duplicates in the seqlevels of your objects so look at seqlevels(ebg) and seqlevels(bamfile). However it's unlikely that you'll see duplicates there either. It looks to me that you've encountered a bug and we would need to be able to reproduce it in order to help. Could you ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Is there a way to tell biocLite() to install a Bioconductor package only if it i
... FWIW setdiff(listOfBiocPackages, rownames(installed.packages())) does the same but is clearer and less typing than listOfBiocPackages[ which( !listOfBiocPackages %in% rownames(installed.packages()) ) ] H. ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 10 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 10 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 11 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 11 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 11 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 11 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 11 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 11 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 12 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Commentator 12 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 14 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 14 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 14 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 24 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 24 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 24 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 24 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 24 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
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