Admin: Hervé Pagès

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Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès

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Comment: C: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... I should add that one benefit of having supportedUCSCtables() use a hard coded list of tables/tracks that are known to be compatible with makeTxDbFromUCSC() is that it makes the function very snappy. Having a smart supportedUCSCtables() that builds that list on-the-fly by querying the Genome Browser ...
written 19 hours ago by Hervé Pagès ♦♦ 12k
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Comment: C: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... Yes hard-coding the mapping between tables and tracks in supportedUCSCtables() is ugly and I welcome any suggestion to improve this. This function has 2 purposes: Provide the list of tables/tracks that are known to be compatible with makeTxDbFromUCSC() Map tables to tracks (many-to-one mapping), ...
written 19 hours ago by Hervé Pagès ♦♦ 12k
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Comment: C: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... You still have access to it. As reported by supportedUCSCtables("hg38") (from GenomicFeatures 1.27.11), this table is now associated to the new UCSC RefSeq subtrack of the composite NCBI RefSeq track. H. ...
written 22 hours ago by Hervé Pagès ♦♦ 12k
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Answer: A: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... Hi Matt, The RefSeq Genes track actually doesn't exist anymore for hg38. It has been replaced with a new composite track named NCBI RefSeq and made of 6 subtracks. See announcement here (from March 3, 2017):   https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome-announce/Prrn-OAFx6U I ju ...
written 1 day ago by Hervé Pagès ♦♦ 12k
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Comment: C: how to transform a list of IRanges into a RangesList instance
... Note that there is also an IRangesList() constructor function that is very similar to RangesList() except that it produces an IRangesList object which is more specific than a RangesList (i.e. the former is a subclass of the latter): IRangesList(lst) # IRangesList of length 3 # [[1]] # IRanges obje ...
written 6 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: Making a gff file for introns to be used with DEXSEQ
... Hi Varun, I'm not familiar with DEXSeq but it seems that the dexseq_count.py script expects a GFF file with features of type exonic_part. This is why you get zero counts with your test.gff file. A quick glance at the vignette seems to indicate that you need to start with a GTF file (containing feat ...
written 15 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Error in GRanges: could not find symbol "recursive" in environment of the generi
... You'll actually have to reinstall from source i.e. with: biocLite(c("BiocGenerics", "S4Vectors", "IRanges", "GenomicRanges"), type="source") which won't work if your system is not set up for doing this. Our Windows and Mac binary packages are not fully compatible with R 3.3.3 yet. We're ...
written 19 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Forge a BSgenome data package
... You're right. I just noticed the OP was using an old BioC and remembered that species went away at some point, but was too lazy to find out exactly when that change was made. So s/he might actually have been looking at an even older version of the BSgenomeForge vignette. Thanks for helping. Thumb u ...
written 19 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: Forge a BSgenome data package
... @Jim: the OP is using an old BioC (3.2). Maybe that's why s/he's putting species in his/her seed file. @jodiera: We don't support old BioC versions. Please update to the current version (BioC 3.4, requires R 3.3). The current version of the BSgenome package is 1.42.0 and the BSgenomeForge vignette ...
written 19 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: "Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter
... Hi, You seem to be using Bioconductor 3.2 which is not supported anymore. Please update your installation to use the current version of Bioconductor (BioC 3.4).  It requires R 3.3 which is also the most current release of R. Thanks, H. ...
written 20 days ago by Hervé Pagès ♦♦ 12k

Latest awards to Hervé Pagès

Scholar 5 weeks ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 8 weeks 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: how much positions overlapped for each pair of the pairs obtained by findover
Scholar 11 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 11 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Scholar 11 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Scholar 11 months ago, created an answer that has been accepted. For A: SNP extraction from SNPlocs.Hsapiens.dbSNP144.GRCh38
Scholar 11 months ago, created an answer that has been accepted. For A: a package for read.fasta
Scholar 11 months ago, created an answer that has been accepted. For A: Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
Scholar 11 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how much positions overlapped for each pair of the pairs obtained by findover
Scholar 11 months ago, created an answer that has been accepted. For A: Requesting flank sequences (BioMart::Exception)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Memory-efficient method to calculate GC content of millions of GRanges
Scholar 11 months ago, created an answer that has been accepted. For A: problem with @ranges@start in DNAStringSet
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 11 months ago, created an answer that has been accepted. For A: resize (shrink/expand) GenomicRanges
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Scholar 11 months ago, created an answer that has been accepted. For A: matching of AAStringSet vs. another AAStringSet
Scholar 11 months ago, created an answer that has been accepted. For A: getting a directed and unweighted adjacency matrix with igraph package

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