Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,567 results • page 2 of 157 • next >
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Comment: C: extracting promoter sequences
... Thx! Now I see the output of sessionInfo() but I don't see a question. The title of your post is "extracting promoter sequences" which gives us a hint of what you're trying to do but you still need to formulate a question somewhere in your post. ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: extracting promoter sequences
... Do you realize that your post is almost impossible to read? ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
... This is actually a new question so it should be asked as such. This way people can find it when they search our support site. The GenomeInfoDb package provides no specific tools for retrieving the assembly gaps. If your assembly is supported by the UCSC Genome Browser, then just import the "gap" ta ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
... Hi Nathan, Have you tried si <- Seqinfo(genome="canFam3"); seqlengths(si) ? It supports many of the most commonly used UCSC assemblies. See ?Seqinfo in the GenomeInfoDb package for more information (don't miss the examples). Let me know if your assembly is not supported and we'll add it. Cheers ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: In GenomicRanges, how to narrow down search of duplicated names in case of "'seq
... Hi, You need to look for duplicates in the seqlevels of your objects so look at seqlevels(ebg) and seqlevels(bamfile). However it's unlikely that you'll see duplicates there either. It looks to me that you've encountered a bug and we would need to be able to reproduce it in order to help. Could you ...
written 3 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Is there a way to tell biocLite() to install a Bioconductor package only if it i
... FWIW setdiff(listOfBiocPackages, rownames(installed.packages())) does the same but is clearer and less typing than listOfBiocPackages[ which( !listOfBiocPackages %in% rownames(installed.packages()) ) ] H. ...
written 4 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: coverage() output SimpleRleList cannot be converted to GRanges
... Hi Xiaotong, Thanks for reporting this. Not sure what "incompatibility between the new IRanges and GenomicRanges packages" you are talking about. To me, it looks like this happens when some list elements in the RleList object representing the coverage have length 0: library(GenomicRanges) cov0 ...
written 4 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: How to find multiple overlaps with pairwiseAlignment()?
... Yes, the code I provided only works if there are only 2 overlapping regions that match with no indels (but mismatches should be ok). I'm afraid generalizing it to support N overlapping regions could get quite complicated... Cheers,   H. ...
written 4 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Unexpected behavior in Biostrings::pairwiseAlignment
... Hi, Note that by default pairwiseAlignments() performs global alignments so in your example the aligned subject is expected to be "--------", not "GATCGATC". Let's use a 1-letter subject: > pa1 <- pairwiseAlignment("GATCGATC", "T") # global > writePairwiseAlignments(pa1) ############### ...
written 4 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Error with makeTxDbFromBiomart in GenomicFeatures package
... Hi Simon, I can reproduce this with the current release version of GenomicFeatures (1.36.2). I tried with various datasets (ddiscoideum_eg_gene, tgondii_eg_gene, pvivax_eg_gene) and all of them gave me the same error that you got. This is actually easy to reproduce with a simple biomaRt query: li ...
written 4 months ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Scholar 5 weeks ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Commentator 12 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
Popular Question 12 months ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
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: subsetByOverlaps with Multimapping
Scholar 12 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 12 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about setdiff() and meta-information in GRanges
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: extract subsequence(s) from DNAStringSet with getSeq
Scholar 12 months ago, created an answer that has been accepted. For A: How do I merge a list of GRanges?
Scholar 12 months ago, created an answer that has been accepted. For A: Generic functions for DataFrames of Rle objects ?
Scholar 12 months ago, created an answer that has been accepted. For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Scholar 12 months ago, created an answer that has been accepted. For A: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
Scholar 12 months ago, created an answer that has been accepted. For A: about setdiff() and meta-information in GRanges
Scholar 12 months ago, created an answer that has been accepted. For A: extract subsequence(s) from DNAStringSet with getSeq
Scholar 12 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 12 months ago, created an answer that has been accepted. For A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Error when running "locateVariants" function in "VariantAnnotation" package
Popular Question 12 months ago, created a question with more than 1,000 views. For overlap regions between two GRanges (or GRangesList)

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