Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 19k
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United States
Website:
http://bioconductor.org/
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12 hours ago
Joined:
11 years, 3 months ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,349 results • page 1 of 235 • next >
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Answer: A: ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
... R's dependency management system should have tried to install AnnotationDbi; but does it help to first say biocLite("AnnotationDbi") before trying GO.db? ...
written 18 hours ago by Martin Morgan ♦♦ 19k
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Comment: C: GO.db will not download
... It sounds like https://support.bioconductor.org/p/92732/ ; can you map the UNC network drive \\nfvfx... to a windows drive letter, launch R from there, and try again? ...
written 1 day ago by Martin Morgan ♦♦ 19k
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Answer: A: About IRanges error
... Does it help to run and correct the problems identified by BiocInstaller::biocValid() ? If not, please EDIT your question to include the output of the R command sessionInfo(), after the error that you report above has occurred. ...
written 1 day ago by Martin Morgan ♦♦ 19k
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Answer: A: translate DNA sequence to Amino acid sequence in a dataframe
... No need to iterate, just translate(DNAStringSet(seq.frame$DNA_seqs)). If you first df=DataFrame(seq.frame) then the result of translate() can be placed in the data frame df$aa = translate(DNAStringSet(df$DNA_seqs)) otherwise use as.character() (again, no iteration) to coerce back to a plain-old-c ...
written 2 days ago by Martin Morgan ♦♦ 19k
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Comment: C: lpsymphony install on Ubuntu
... FWIW I wonder if what you've provided actually includes the error; they look like warnings that would not normally lead to an error. ...
written 4 days ago by Martin Morgan ♦♦ 19k
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Answer: A: Can't download WGCNA
... I'm not exactly sure of the details, but I think you could map the network drive (google led me to here, but there might be better instructions) where R is installed, and launch R from the mounted drive rather than the network location. Then try the problematic command BiocInstaller::biocLite("GO. ...
written 4 days ago by Martin Morgan ♦♦ 19k
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Answer: A: BiocParallel on Windows: how should I pass (not exported) setReplace functions t
... You're asking about package development, and the right forum for that is the bioc-devel mailing list. I guess this is your MIGSA package. What's an easily reproduced example showing the error? Modulo special circumstances, packages using non-exported methods should 'just work' for the reasons outli ...
written 6 days ago by Martin Morgan ♦♦ 19k
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Answer: A: BiocParallel on Windows : cannot find my functions when using SnowParam
... Linux / MacOS default to MulticoreParam(). Windows doesn't support MulticoreParam(), so defaults to SnowParam(). MulticoreParam() uses a 'shared memory' model where the workers share the memory of the calling parent, so automatically 'know' about functions that are defined in the manager R session. ...
written 6 days ago by Martin Morgan ♦♦ 19k
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Answer: A: issue with version compatibility
... Version 3.4, the version you have installed and the most recent 'release' version of Bioconductor, works with R version 3.3.2. You were able to install airway (see your script!) with this version of Bioconductor, so you are mis-diagnosing your problem. ...
written 6 days ago by Martin Morgan ♦♦ 19k
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Comment: C: not able to install bioconductor packages
... This is a different question, so start a new support site question. But review first the error message -- an object 'sampleTable' is not found in your R session -- and the script that I guess you are trying to follow, and ask how R should know about the object sampleTable. ...
written 6 days ago by Martin Morgan ♦♦ 19k

Latest awards to Martin Morgan

Scholar 16 days ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 10 months ago, created an answer that has been accepted. For A: Submitting an experimental data package
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Get source code for rpkm() function in edgeR
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to convert a GRangesList object into a GRanges object?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to access Emsembl plants with biomaRt
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about filtering variants in a VCF file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: countOverlaps with weights
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Codelink annotation error in Ubuntu 16.04
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Offline loading of BiocInstaller or depending packages and connection timeout
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: Cannot install CummeRbund on R v.3.3.0
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: finding overlapping regions within 2 different bed files with different features
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Load balancing using BiocParallel
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: bplapply stalling upon error with large data objects
Scholar 10 months ago, created an answer that has been accepted. For A: scanBam with ScanBamParam argument which specified ignores yieldSize. Intentiona
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: scanBam on BamSampler supposed to be fast?
Scholar 10 months ago, created an answer that has been accepted. For A: scanBam on BamSampler supposed to be fast?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Plotting only intergenic reads on chromosomes?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: getting the longest transcript by gene from Refseq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: IRanges, Partitioning by End function not found.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: BPPARAM = bpparam() takes longer than using BPPARAM = SerialParam()
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering a BAM file using RSamtools
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Any way to proceed duplicate removal for list of GRanges object ?
Scholar 10 months ago, created an answer that has been accepted. For A: Long elapsed time using `import.gff3` with a toy example
Scholar 10 months ago, created an answer that has been accepted. For A: bplapply stalling upon error with large data objects

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