Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

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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 2 days 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 5 days 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 14 days 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 14 days 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 15 days 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 23 days ago by Hervé Pagès ♦♦ 13k
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Comment: C: GenomicFeatures and custom genomes?
... Just realizing now that extractUpstreamSeqs() doesn't take a DNAStringSet object, sorry. We should add this at some point. So for now you could either use: library(Rsamtools) genome <- FaFile(fasta_file) as Martin suggested, or convert your FASTA file to 2-bit format with something like: ex ...
written 4 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: GenomicFeatures and custom genomes?
... Hi, Using extractUpstreamSeqs() from the GenomicFeatures package: library(Biostrings) genome <- readDNAStringSet(fasta_file) library(GenomicFeatures) txdb <- makeTxDbFromGFF(gtf_file) extractUpstreamSeqs(genome, txdb) If you have a 2-bit file instead of FASTA, replace genome <- readDNA ...
written 4 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Problem installing BiocGenerics
... Hi, I can't reproduce this either. Glad that installing R 3.4.2 Patched solved the problem. If you still have your R 3.4.2 installation around, could you start it and show us the output of methods:::.standardGenericDots? FWIW I just made a small change to the hotfix code to improve the error messa ...
written 4 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: CDS phase information missing from GenomicFeatures
... FYI I made a first pass on this: in GenomicFeatures 1.29.14, makeTxDbFromGFF() and makeTxDbFromGRanges() now import the CDS phase: https://github.com/Bioconductor/GenomicFeatures/commit/22b2ea0a81bc064b8554400ce8f7e13e2c833d38 Was actually not that bad. cdsBy(txdb, by="tx") still needs to be modif ...
written 4 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

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: Extracting Coordinates of startcodon from Grangeslist
Scholar 5 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 6 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 6 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 6 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 6 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 7 months ago, voted at least 25 times.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 7 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Commentator 7 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 9 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
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
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 19 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 19 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 19 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 19 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 19 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

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