Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,552 results • page 2 of 156 • next >
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Answer: A: Error in pairwiseAlignment when considering an empty seuqnece
... Hi Kristoffer, Sorry that it took so long but this was a low-priority issue. It should be fixed in Biostrings 2.47.3: library(Biostrings) pattern <- DNAString("ATCG") subject <- DNAString("") pairwiseAlignment(pattern, subject) # Global PairwiseAlignmentsSingleSubject (1 of 1) # pattern: [1 ...
written 5 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Intergenic coordinates with Genomic Feaures
... FWIW you can get the subset of ranges in resMa that overlap with at least one intergenic region with subsetByOverlaps(resMa, intergenicRegions2). So you could just show us the output of head(subsetByOverlaps(resMa, intergenicRegions2)) plus your sessionInfo(). Thanks! ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: create a txdb using makeTxDbFromGFF
... sessionInfo() please! Your version of Bioconductor seems outdated. Note that makeTxDbFromGFF() uses rtracklayer::import.gff3() internally as a first step of importing the GFF3 file as a GRanges object. And even though the sequence lengths are present in the file, for some reasons rtracklayer::impor ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Query with Biostrings pairwise alignment output positon
... Hi Dhwani, 1) One possible explanation for the discrepancy with Emboss needle is that pairwiseAlignment() interprets gapOpening as the cost of opening the gap only. This differs from other alignment software where it's the cost of the first dash ("-") in the gap. Have a look at writePairwiseAlignme ...
written 9 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Found more than one class
... Yes, your sessionInfo() would help me reproduce this. Right now I can't. ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: From RleList to RleArray
... Thanks for the PR Pete. I just merged it.  H. ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: unlist a exons GRangeslist object and add a gene name column
... Hi, The gene ids are stored in the names of the GRangesList object: ex_by_gene <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene,   by="gene") names(ex_by_gene)[1:3] # [1] "1"   "10"  "100" Unlisting doesn't loose them: exons <- unlist(ex_by_gene) names(exons)[1:29] # [1] ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
... Hi, A TxDb object can represent a polycistronic transcript only if it is "split" i.e. if it is assigned more than one transcript ID. Note that this "split" is what the major annotation providers seem to be doing e.g. NCBI reports 6 mRNAs for Entrez gene 114548 but NM_004895 and NM_001243133 actuall ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: ChIPQC Error in .Call2 NCList object is too deep
... Hi Thomas, The current implementation of NCList and GNCList objects imposes a hard-coded limit of 100000 nested ranges. Note that you hit this limit only when you build an NCList or GNCList object by explicitly calling the NCList() or GNCList() constructor. Most of the time this is not necessary th ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Cannot extract TxFeatures for a defined GRanges object
... Hi, As discussed on the bioc-devel mailing list in this thread: https://stat.ethz.ch/pipermail/bioc-devel/2017-October/012215.html there seems to be a problem with the BioMart service that causes part of the data requested by makeTxDbFromBiomart() to get lost while on its way from Ensembl to the ...
written 3 months ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 9 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 9 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
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
Scholar 10 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 10 months ago, voted at least 25 times.
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: A bug of "seqlevels<-" on TxDb
Commentator 10 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 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
Scholar 12 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 22 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 22 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 22 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 22 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 22 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

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