Admin: Hervé Pagès

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Hervé Pagès ♦♦ 14k
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13 years, 10 months ago
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Posts by Hervé Pagès

<prev • 1,680 results • page 1 of 168 • next >
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Comment: C: Error in creating BSGenome package
... Not sure what's going on exactly but the fact that you have ``` seqs_srcdir:/ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/ ``` in your seed file does not look good. As explained in the vignette, the `seqs_srcdir` folder must be local: > So we assume that you've downloaded the _seq ...
written 2 days ago by Hervé Pagès ♦♦ 14k
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Answer: C: Can GenomicRanges findOverlaps ignore seqnames?
... Just set the seqnames of all the ranges in the query and subject to the same value. This can be done with something like: ``` library(GenomicRanges) example(GRanges) GRanges("A", ranges(gr), strand(gr)) # GRanges object with 10 ranges and 0 metadata columns: # seqnames ranges strand # ...
written 8 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Error: 'exprs<-' is not an exported object from 'namespace:affy'
... FYI this `R CMD check` bug has been fixed in R-devel: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17613 ...
written 15 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Problem in installing maEndToEnd package
... Problem with using `dependencies=c("Depends", "Imports", "LinkingTo", "Suggests","Enhances")` is that it tends to install way to many packages, and many of them are actually never used/needed by the package that you're trying to install (in this case maEndToEnd). This is the case for statnet. It's n ...
written 18 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Assembly report error for hg19 in GenomeInfoDb
... Hi, 2 problems with your post: 1. The tag you used (software error) is too general. Please use a package specific tag (GenomeInfoDb in this case). This will help other users of the support site find questions/answers about the package and will notify the GenomeInfoDb maintainers that a questions ...
written 18 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Error when installing Rgraphviz on Centos
... The tag you used (software error) is too general and the Rgraphviz maintainers won't necessarily pay attention to a post with such a general tag. Since this is about an installation error with the Rgraphviz package, I'd suggest you tag your post with Rgraphviz. ...
written 19 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Error on Rhtslib package installation
... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib Cheers, H. ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib Cheers, H. ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Rhtslib - install error
... Rhtslib 1.16.2 is now available: https://bioconductor.org/packages/3.9/Rhtslib Also please make sure that you have libbz2 + liblzma + header files on your system. On a Debian-based Linux system like Ubuntu these can be installed with `sudo apt-get install libbz2-dev liblzma-dev`. Cheers, H. ...
written 25 days ago by Hervé Pagès ♦♦ 14k
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Comment: C: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
... I backported the fix yesterday to Rhtslib 1.16.2. Rhtslib 1.16.2 should become available via `BiocManager::install()` in the next 24h or so. Best, H. ...
written 29 days ago by Hervé Pagès ♦♦ 14k

Latest awards to Hervé Pagès

Popular Question 9 weeks ago, created a question with more than 1,000 views. For how to obtain base counts from BAM file at specific genomic coordinates
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rsamtools v 1.99.6 installation error
Popular Question 9 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 9 months ago, created an answer that was upvoted at least 5 times. For A: resize (shrink/expand) GenomicRanges
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rsamtools v 1.99.6 installation error
Scholar 9 months ago, created an answer that has been accepted. For A: Rsamtools v 1.99.6 installation error
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Popular Question 9 months ago, created a question with more than 1,000 views. For RSQLite installation question
Scholar 9 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Popular Question 9 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 9 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 9 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Good Answer 10 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 13 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 13 months ago, created an answer with at least 3 up-votes. For A: Calling coverage on GRanges object yields small negative values
Scholar 13 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 13 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question 13 months ago, created a question with more than 1,000 views. For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Popular Question 13 months ago, created a question with more than 1,000 views. For unique, duplicated, order, etc... on a GRanges object
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 16 months ago, created an answer that has been accepted. For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar 16 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist

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