Admin: Hervé Pagès

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Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès

<prev • 1,513 results • page 1 of 152 • next >
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Comment: C: Biomart ensembl annotation does not completely match my gene names
... Hi, A few things that might help understand what's going on: What's "biomart ensembl hgnz_names"? I see attributes hgnc_id, hgnc_symbol, and hgnc_trans_name in the hsapiens_gene_ensembl dataset of the ENSEMBL_MART_ENSEMBL mart. Is this what you are talking about? Where did you get your 29581 HUGO ...
written 1 day ago by Hervé Pagès ♦♦ 12k
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Answer: A: BSgenomeForge error in .TwoBits_export
... I see. It looks like the BSgenome.Hsapiens.NCBI.GRCh38.p11 destdir got created but not the inst/extdata/ folder below it. This should be fixed in BSgenome 1.44.2. The fix should take between 24-48 hours to become available via biocLite(). Sorry for the inconvenience, H. ...
written 1 day ago by Hervé Pagès ♦♦ 12k
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Answer: A: Implementing fast mathematical and statistical operations on genomic variables i
... Hi Devin, Just a heads up that the plan is to move away from the named RleList representation or the disjoint GRanges with metadata columns for representing genomic variables. In a not too distant future genomic variables will be better represented as metadata columns on a GPos object. Note that t ...
written 2 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: reads alignment statistics
... Hi, The quickBamFlagSummary() function in Rsamtools will display various stats about the FLAG field. For example: > quickBamFlagSummary(bamfile) | | | mean / max                           group |    nb of |   nb of | records ...
written 2 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: BSgenomeForge error in .TwoBits_export
... Hi Lena, Not sure what's going on. But I wonder what these RRBS_spike-in_* sequences are and where you downloaded the RRBS_spike-in_*.fa files from. The source_url field you provide points to a folder that contains the GCF_000001405.37_GRCh38.p11_genomic.fna.gz file (this is a FASTA file that conta ...
written 2 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: Accessing SNP datasets from NCBIM37 on biomaRt
... Hi, AFAIK SNP information for mouse can be found in different places via biomaRt: 1. In the snp_chromosome_strand attribute of the mmusculus_gene_ensembl dataset of the ENSEMBL_MART_ENSEMBL mart: > library(biomaRt) > mart <- useMart(host="may2012.archive.ensembl.org",   ...
written 2 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: remove NA's from a DelayedArray
... I added this to DelayedArray 0.3.20: library(DelayedArray) A <- DelayedArray(matrix(c(NA, 1:10, NA), ncol=3)) A[is.na(A)] <- 0 A # DelayedMatrix object of 4 x 3 doubles: # [,1] [,2] [,3] # [1,] 0 4 8 # [2,] 1 5 9 # [3,] 2 6 10 # [4,] 3 7 0 DelayedArra ...
written 3 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: remove NA's from a DelayedArray
... After more thoughts on this, I think we can support delayed subassignment (i.e. x[i] <- value) at least in the special case where: (1) i is a logical DelayedArray with the same dimensions as x, and (2) value is a scalar (i.e. atomic vector of length 1). That would cover x[is.na(x)] <- 0 but al ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: remove NA's from a DelayedArray
... Hi, I need to think of a more natural/intuitive way to support this but in the mean time you can use the following: replaceNAs <- function(x, value) { stopifnot(is(x, "DelayedArray"), is.vector(value), is.atomic(value), length(value) == 1L) Del ...
written 4 days ago by Hervé Pagès ♦♦ 12k
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Answer: A: Errors with makeTxDbFromBiomart
... Hi Gnanendra, Thanks for reporting this problem. Note that you should always tag your question with the package that is causing problem, which in this case is the GenomicFeatures package (where the makeTxDbFromBiomart() function belongs). The problem should now be fixed in GenomicFeatures 1.28.5. ...
written 4 days ago by Hervé Pagès ♦♦ 12k

Latest awards to Hervé Pagès

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: Extracting Coordinates of startcodon from Grangeslist
Scholar 3 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 4 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 4 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 4 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 4 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 4 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 5 months ago, voted at least 25 times.
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
Commentator 5 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 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
Scholar 7 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 17 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 17 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 17 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 17 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 17 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

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