User: Henrik Bengtsson

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Posts by Henrik Bengtsson

<prev • 248 results • page 1 of 25 • next >
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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 8 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 22 months 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 22 months 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 22 months 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 3.4 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 3.4 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 3.4 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 3.5 years ago by Henrik Bengtsson2.4k
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Answer: A: A parser for Tiled Data File (TDF) format?
... As a follow up to my own question, I've found that Java class org.broad.igv.tdf.TDFUtils part of IGV to some extent can be used to parse TDF files. For instance, one can convert a TDF to a BED file from within R as: > library("rJava") > .jinit(classpath="igvtool.jar") > TDFUtils <- .jn ...
written 3.5 years ago by Henrik Bengtsson2.4k
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Is there an R package providing an R API for IGV / igvtools out there?
... Does anyone know of an R package (on CRAN, Bioconductor, GitHub or elsewhere) that provides an R API to igvtools? It's quite easy to use an existing igvtools.jar built and distributed by the Broad Institute, e.g. > library("rJava") > .jinit(classpath="igvtool.jar") > TDFUtils <- .jnew( ...
package igv written 3.5 years ago by Henrik Bengtsson2.4k • updated 3.5 years ago by Paul Shannon370

Latest awards to Henrik Bengtsson

Popular Question 8 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 10 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 22 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 22 months 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 3.2 years ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Rsamtools: sortBam() and 'samtools sort' does not give the same results
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Scholar 3.7 years ago, created an answer that has been accepted. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Centurion 13.0 years ago, created 100 posts.

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