Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
Reputation:
22,790
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United States
Website:
http://bioconductor.org/
Last seen:
12 hours ago
Joined:
13 years, 5 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,102 results • page 1 of 311 • next >
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Answer: A: GSEABase: how to extract shortDescription from GeneSetCollection object
... Instead of looking at the structure of the object, I looked at the methods available (not completely foolproof...) example(readGmt) methods(class = class(gss[[1]])) and then found description(gss[[1]]) I guess I was hoping that `?"description,GeneSet-method"` would actually be helpfu ...
written 15 hours ago by Martin Morgan ♦♦ 23k
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Answer: A: New to bioinformatics
... [Modern Statistics for Modern Biology][1] with its many bioinformatic ties might for a great connection between your statistical training and bioinformatic data. [1]: https://www.huber.embl.de/msmb/ ...
written 18 hours ago by Martin Morgan ♦♦ 23k
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Answer: A: DataFrame after splitting and back
... Maybe DataFrame(lapply(df2, unsplit, df$k)) ? ...
written 22 hours ago by Martin Morgan ♦♦ 23k • updated 22 hours ago by Michael Lawrence11k
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Comment: C: seqCAT profiler filtering out all variants?
... I believe that this is a bug fixed in Rhtslib 1.15.6, but I am not exactly sure because your packages seem a mix of release and 'devel' versions. Be sure that `BiocManager::valid()` returns TRUE. ...
written 1 day ago by Martin Morgan ♦♦ 23k
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Comment: C: ExperimentHub downloading files to home directory (~)
... See also `?setExperimentHubOption` for setting the cache to an arbitrary location via `EXPERIMENT_HUB_CACHE` as a system environment variable, as an R option, or through the ExperimentHub interface. ...
written 15 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Error in ncol(eset) 'eset.filt' not found
... Your statement that genefilter is not available for R-3.5.3 is not correct. Have you tried to install it using the instructions on the [package landing page][1]? ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("genefilter", version ...
written 18 days ago by Martin Morgan ♦♦ 23k
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Comment: C: BioC2018 Workshop book not linked from Bioconductor.org?
... yes we're aware of that! probably as you say bioconductor.github.io/BiocWorkshops will point either to the current version with link to previous versions, or an overall page with links to current and past versions. ...
written 20 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Issue setting up BiocManager due to mgcv / clang?
... The file needs to be `Makevars`, without the `.txt` extension. ...
written 21 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Compare and filter two BAM files, one record at a time
... There is an argument `indexDestination=` to `filterBam()`; set it to FALSE? ...
written 23 days ago by Martin Morgan ♦♦ 23k
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Answer: A: Iterating over BAM file by genomic chunk
... Using `yieldSize=1L` with a `ScanBamParam()` having a `which=` field iterates over ranges ``` fl = system.file(package="Rsamtools", "extdata", "ex1.bam") bam = BamFile(fl, yieldSize = 1) param = ScanBamParam( which = GRanges(c("seq2:1-1000", "seq1:1-1000")) ) open(bam) repeat { aln = readG ...
written 23 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Appreciated 4 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 5 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 5 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Scholar 6 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 6 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 6 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 8 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 10 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 10 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Popular Question 10 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 10 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar 10 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 11 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 11 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 22 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file

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