Admin: Hervé Pagès

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Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès

<prev • 1,618 results • page 1 of 162 • next >
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Answer: A: BiocCheck package size
... This question is about package development hence should be asked on the bioc-devel mailing list: https://stat.ethz.ch/mailman/listinfo/bioc-devel Thanks, H. ...
written 3 hours ago by Hervé Pagès ♦♦ 13k
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Answer: A: DataFrame compatible left_join (merge) operation supporting S4 complex columns t
... Hi, A workaround is to perform your own merge e.g. with something like this: ``` library(S4Vectors) x <- DataFrame(tx_id=letters[1:7], gene_id=c(3, 19, 4, 1, 1, 3, 1)) y <- DataFrame(gene_id=1:5, gene_name=LETTERS[1:5]) m <- match(x$gene_id, y$gene_id) cbind(x, y[m, ]) # DataFrame with 7 r ...
written 3 days ago by Hervé Pagès ♦♦ 13k
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Comment: C: getSeqSrcpaths (forgeBSgenome) error files not found, but they are right there..
... Please edit your post to make proper use of markdown so underscores and other important characters don't disappear. For example wrap file paths and R expressions in backquotes (`` ` ``) so we can see exactly what they look like and even copy/paste them in our own R sessions. This should give somethi ...
written 21 days ago by Hervé Pagès ♦♦ 13k
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Comment: C: Error in VCF parsing with VariantAnnotation
... `sessionInfo()` please? Thanks ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Obtain coordinates of 5' upstream region up to closest coding region
... And FWIW here is the fast version of it: ``` trimFivePrimeSide <- function(gr, remove) { stopifnot(is(gr, "GenomicRanges"), is(remove, "GenomicRanges")) mapping <- as(findOverlaps(gr, remove), "IntegerList") new_start_on_plus_strand <- pmin(max(extractList(end(remove), ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Create protein sequences including variants from a VCF file
... FWIW you might also want to take a look at `Biostrings::replaceAt()`. It's lower level and more flexible than `BSgenome::injectSNPs()` (the former works on AAString/AAStringSet/DNAString/DNAStringSet objects while the later only works on a BSgenome object). ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Obtain coordinates of 5' upstream region up to closest coding region
... Hi, So IIUC, for each gene you want the longest upstream region that is <= 2kb and does not overlap with any known CDS. Or, said otherwise, you want to minimally trim (on the 5' side) the upstream regions in `gnflanks` so that they are CDS-free. Note that this trimming will sometimes result in a ...
written 6 weeks ago by Hervé Pagès ♦♦ 13k
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Answer: A: Using GenomicFeatures to extract the upstream and downstream region of a transcr
... Hi, Please be aware that some familiarity with R is highly recommended before you can efficiently use Bioconductor. It's not clear to me whether you want to extract the upstream and downstream _regions_ (i.e. their coordinates with respect to the reference genome) or the _genomic sequences_ (DNA) ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: GenomeInfoDb's Seqinfo() error on hg38
... BTW this change was finally announced recently on the Genome Browser's blog: http://genome.ucsc.edu/blog/patches/ and on their mailing list: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome-announce/oMMnhnPr6gg The hg38 gateway page still doesn't say what assembly the hg38 tracks ar ...
written 7 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: GenomeInfoDb's Seqinfo() error on hg38
... Should be fixed in GenomeInfoDb 1.19.2 (devel, see commit [here]( https://github.com/Bioconductor/GenomeInfoDb/commit/18c1056adb2304b0e194df31acbf061c6f6ec04b)) and 1.18.2 (release). These new versions won't show up on the build reports ([devel](https://bioconductor.org/checkResults/devel/bioc-LATES ...
written 10 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 3 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: how to extract "Gene type" from org.Mm.eg.db?
Popular Question 7 months ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Popular Question 7 months ago, created a question with more than 1,000 views. For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Scholar 7 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Popular Question 7 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Scholar 7 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 11 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 11 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 11 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 11 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: extract subsequence(s) from DNAStringSet with getSeq
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: about setdiff() and meta-information in GRanges
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Error when running "locateVariants" function in "VariantAnnotation" package
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 22 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
Commentator 22 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

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