Admin: Hervé Pagès

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Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès

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Comment: C: Possible issue with Rsamtools ScanBamParam mapqfilter
... Hi, I would need to be able to reproduce this error in order to troubleshoot. Do you think you can make your BAM file available somewhere? Or a subset of it only as long as it allows me to reproduce the error. Thanks! H. ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: add annotation features to BSgenome or txdb package
... Hi D., If there is no OrgDb package for your non model organism, and you need one, then I guess you'd want to make one. Not clear to me why you'd want to put these annotations in a BSgenome data package. These packages are meant for the genome sequences. Could you clarify what you are trying to do? ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: reduce function in GenomicRanges
... Oh I see now why you expected ranges chr1:5-10 and chr1:95-101 to be merged. Sorry for missing that. I modified my answer above to support the min.gapwidth argument. Also fixed a bug in circularReduceIRanges(). Cheers, H. ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: reduce function in GenomicRanges
... [Edited on Jul 23, 2017: Simplified and fixed bug in circularReduceIRanges(). Also added the min.gapwidth argument.] Hi, Indeed, reduce() does not handle circularity yet. The circularReduceGRanges() function below implements a circularity-aware reduction for GRanges objects: seqinfo <- Seqin ...
written 6 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: CAGEr BAM files size issue
... Hi, You're using the CAGEr package so I'm not sure exactly how the Biostrings package could help you solve this issue. Unless I add support for long XString objects, which is on the radar but unlikely to happen in the near future. In the mean time, one way to solve the issue would be to revisit the ...
written 6 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: CAGEr BAM files size issue
... Hi, The error message is coming from Biostrings and is admittedly not helpful. I just changed this in Biostrings 2.44.2 and now it says: > unlist(big_dna_string_set) Error in .Call2("XStringSet_unlist", x, PACKAGE = "Biostrings") : XStringSet object is too big to be unlisted (would result i ...
written 7 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: makeTxDbFromGFF Error due to incompatible seqnames
... Hi, Something looks wrong with your GTF file. Do you think you can make it available somewhere so we can look at it? Thanks, H. ...
written 7 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: How to suppress the out-of-bound warnings in GenomicRanges function resize()
... By wrapping the call generating the warning inside suppressWarnings(). This is the standard way to suppress warnings in R. See ?suppressWarnings for more information. Cheers, H. ...
written 8 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Does package S4Vectors break ifelse?
... Hi, Michael replaced the ifelse generic and methods with a new ifelse2 generic and methods in IRanges 2.11.8.  So AFAICT no Bioconductor package defines any ifelse method anymore. Cheers, H. ...
written 9 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Is there any package helps finding Tandem Repeats ?
... Hi, The little findTandemRepeats() function I provided above is designed to work on a DNAString object so all you need to do is load the Biostrings package and turn your raw sequence into a DNAString object before calling findTandemRepeats on it: library(Biostrings) findTandemRepeats(DNAString("A ...
written 9 days ago by Hervé Pagès ♦♦ 12k

Latest awards to Hervé Pagès

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 8 weeks ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 10 weeks ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 10 weeks ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 11 weeks ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 12 weeks 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
Supporter 3 months ago, voted at least 25 times.
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
Commentator 3 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 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: A bug of "seqlevels<-" on TxDb
Scholar 5 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 15 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 15 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 15 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 15 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 15 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

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