User: Henrik Bengtsson

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Posts by Henrik Bengtsson

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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 12 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 12 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 12 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 2.6 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 2.6 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 2.6 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 2.6 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 2.6 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 2.6 years ago by Henrik Bengtsson2.4k • updated 2.6 years ago by Paul Shannon360
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A parser for Tiled Data File (TDF) format?
... Hi, does anyone know of a parser, preferably in R, for the Tiled Data File (TDF) format that is used by the Broad's IGV Browser? The TDF format is binary, but appears to be poorly documented.  It looks like it is mostly intended as an intermediate file format to speed up IGV, and the Broad's igvtoo ...
igv file format parser io tdf written 2.6 years ago by Henrik Bengtsson2.4k

Latest awards to Henrik Bengtsson

Popular Question 11 months ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 11 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 2.3 years ago, created a question with more than 1,000 views. For R 2.15.1 ReadAffy error
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Rsamtools: sortBam() and 'samtools sort' does not give the same results
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Scholar 2.8 years ago, created an answer that has been accepted. For A: Error aroma.affymetrix [affxparser Fusion SDK exception]
Centurion 12.2 years ago, created 100 posts.

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