User: Henrik Bengtsson

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Posts by Henrik Bengtsson

<prev • 250 results • page 1 of 25 • next >
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Comment: C: R 3.6.1: How to upgrade from existing Bioconductor 3.9 to 3.10?
... Ah... I see. Thxs I'd like to suggest that a section on 'Upgrading from a previous Bioconductor version' with this is added to [https://bioconductor.org/install/][1] [1]: https://bioconductor.org/install/ ...
written 5 weeks ago by Henrik Bengtsson2.4k
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R 3.6.1: How to upgrade from existing Bioconductor 3.9 to 3.10?
... I realize I don't know what the official way to upgrade an existing Bioconductor 3.9 on R 3.6.1 to Bioconductor 3.10, which was released yesterday (2019-10-30). I've looked at [https://bioconductor.org/news/bioc_3_10_release/][1] and [https://bioconductor.org/install/][2] but I don't think they say ...
upgrade biocmanager written 5 weeks ago by Henrik Bengtsson2.4k • updated 5 weeks ago by Martin Morgan ♦♦ 24k
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Comment: C: A parser for Tiled Data File (TDF) format?
... Don't know, haven't tried for a long time. But, try to use a path without ~, e.g. normalize it with normalizePath(...). ...
written 12 months ago by Henrik Bengtsson2.4k
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Comment: C: DOI for packages
... Ah, great. Just checked, so for instance https://bioconductor.org/packages/betr will redirect to https://bioconductor.org/about/removed-packages/ listing all removed packages.  There one easily finds a link to https://bioconductor.org/packages/3.4/bioc/html/betr.html - the most recent release before ...
written 2.1 years ago by Henrik Bengtsson2.4k
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Comment: C: DOI for packages
... Great. Thxs. Future-looking question: To what will the DOI point to when a Bioc package is deprecated and archived, i.e. when there's no longer a landing page for that package? ...
written 2.1 years ago by Henrik Bengtsson2.4k
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Answer: A: defaults in BiocParallel
... Stumbled upon this old thread.  I fully agree with Kasper here (if this is still his position).  Scientific software, including R packages, that defaults to "hijacking" whatever cores are available on a machine are likely to cause problems on multi-tenant environments such as compute cluster, but al ...
written 2.2 years ago by Henrik Bengtsson2.4k
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Comment: C: DNAString: Standard checksum function?
... I would favor long enough checksums to minimize the risk for collisions; the cost for troubleshooting when there are collisions is much higher.  It's fairly simple to memoize/cache results to file. > Right now different DNA sequence databases use different sequence IDs but it would be great if t ...
written 3.7 years ago by Henrik Bengtsson2.4k
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Answer: A: DNAString: Standard checksum function?
... I found the following presentation: Bassi, Sebastian and Gonzalez, Virginia. New checksum functions for Biopython. Available from Nature Precedings, 2007 Abstract: Checksum algorithms are used in biological databases for integrity check and identification purposes. CRC64 is the only checksum algor ...
written 3.7 years ago by Henrik Bengtsson2.4k
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DNAString: Standard checksum function?
... Hi, in a reverse-engineering task, I'd like to compare the content of two FASTA files (for which I cannot trace the origin).  When comparing the FASTA index files, the sequence/chromosome names as well as the lengths of the individual sequences agree, although in a different order.  Next I'd like t ...
sequencing biostrings fasta written 3.7 years ago by Henrik Bengtsson2.4k
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Comment: C: Is there an R package providing an R API for IGV / igvtools out there?
... Thanks Paul, this looks promising.  I should have been a bit more clear in my question.  I'm looking for an access that does not require a separate installation of IGV.  In your case you seem to connect to a running instance of IGV via sockets.  I'm basically looking for a direct access to the Java ...
written 3.8 years ago by Henrik Bengtsson2.4k

Latest awards to Henrik Bengtsson

Popular Question 12 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 14 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Is there an R package providing an R API for IGV / igvtools out there?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Rsamtools: sortBam() and 'samtools sort' does not give the same results
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Scholar 4.0 years ago, created an answer that has been accepted. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Centurion 13.3 years ago, created 100 posts.

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