Admin: Hervé Pagès

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Hervé Pagès ♦♦ 14k
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Posts by Hervé Pagès

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Comment: C: New Bioconductor package for dbSNP151
... Hi Jesper, Thanks for the positive feedback. Very appreciated and motivating! In BioC devel ([BSgenome 1.55.2](https://github.com/Bioconductor/BSgenome/commit/c583eea987185cd5cdd16ebc6a66c70913a27136)) I've improved the SNPlocs extractors to return the **inferred** ref allele and alt allele(s): `` ...
written 1 day ago by Hervé Pagès ♦♦ 14k
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Comment: C: Problem installing BSgenome packages with R 3.6.1
... Hi, I see "Installation path not writeable" in the error messages you're showing us so I wonder: Can you install any package at all? Try something like: ``` install.packages("mgcv") ``` If this fails then your problem does not have much to do with the BSgenome.Hsapiens.UCSC.hg19 package or with Bio ...
written 3 days ago by Hervé Pagès ♦♦ 14k
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Answer: A: Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
... BSgenome.Mmulatta.UCSC.rheMac10 is now available. See https://support.bioconductor.org/p/126958/ Cheers, H. ...
written 7 days ago by Hervé Pagès ♦♦ 14k
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News: New BSgenome data packages for bosTau9, rheMac10, danRer11, and galGal6
... Hello Bioconductor citizens, New BSgenome data packages are now available in release (BioC 3.10) and devel (BioC 3.11) for UCSC assemblies bosTau9 (Cow), rheMac10 (Rhesus), danRer11 (Zebrafish), and galGal6 (Chicken): - https://bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau9 - https://bioc ...
bsgenome news written 7 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Can't find library BSgenome.Mmulatta.UCSC for latest genome (mmul10)
... Right. Although it's not exactly the same. The BSgenome wrapper adds a few conveniences like the ability to rename the seqlevels, "inject" SNPS, properly handle circular sequences, and a cleaner sequence order. Also not all workflows support TwoBitFile objects (even though they probably should). No ...
written 9 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Question: Easy way to fetch the first exons from genome
... I don't know. This sounds like is a slightly different topic though so I would recommend that maybe you try to ask this as a new question. ...
written 24 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Question: Easy way to fetch the first exons from genome
... One more thing (and I'll stop replying to myself). The very first exon in each gene can actually be obtained more simply with: ``` ex_by_gene <- exonsBy(txdb, by="gene") gene_strand <- as.character(unique(strand(ex_by_gene))) idx <- ifelse(gene_strand == "+", which.min(start( ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Question: Easy way to fetch the first exons from genome
... I should add that the fact that some genomic ranges are repeated multiple times in `first_exons` (e.g. the first 3 exons are the same) simply reflects the fact that several transcripts in a gene can share the same first exon. So if you're interested in knowing the location of the first exon for each ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Question: Easy way to fetch the first exons from genome
... A gene has one TSS per transcript. You can easily get the 1st exon of each known transcript by extracting the exons grouped by transcript: ``` library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene ex_by_tx <- exonsBy(txdb, by="tx") ex_by_tx # GRangesList obje ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Answer: A: Question: Easy way to fetch the first exons from genome
... Hi, How about extracting the exons from a TxDb object and pick up the "first exons"? (whatever that means): ``` library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene ex <- exons(txdb) ex # GRanges object with 76920 ranges and 1 metadata column: # ...
written 4 weeks ago by Hervé Pagès ♦♦ 14k

Latest awards to Hervé Pagès

Popular Question 4 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Rsamtools v 1.99.6 installation error
Popular Question 11 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: resize (shrink/expand) GenomicRanges
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Rsamtools v 1.99.6 installation error
Scholar 11 months ago, created an answer that has been accepted. For A: Rsamtools v 1.99.6 installation error
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Popular Question 11 months ago, created a question with more than 1,000 views. For RSQLite installation question
Scholar 11 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Popular Question 11 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 11 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: how to extract "Gene type" from org.Mm.eg.db?
Appreciated 12 months ago, created a post with more than 5 votes. For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Popular Question 14 months ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 14 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 14 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question 14 months ago, created a question with more than 1,000 views. For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Popular Question 14 months ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 18 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 18 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
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