Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
Reputation:
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http://bioconductor.org/
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4 hours ago
Joined:
13 years, 11 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,254 results • page 2 of 326 • next >
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Comment: C: How to build and map to a "pre-mRNA" reference transcriptome for single nucleus
... I think implicit in the question is the desire to do this in or with R / Bioconductor, so the question is appropriate here. ...
written 11 days ago by Martin Morgan ♦♦ 23k
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Comment: C: DESeq2 using many cores despite parallel = FALSE
... you could try `trace(bplapply)` (or maybe `trace(BiocParallel::bplapply)`) before running `estimateSizeFactors()`; you'll see a trace print every time `bplapply()` is evaluated. You could also add an expression to `trace()` to document how `bplapply()` is being called... ``` > trace(bplapply, qu ...
written 11 days ago by Martin Morgan ♦♦ 23k
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Comment: C: FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(f
... Can you share enough of the VCF file so that I can reproduce this? It might also help to name your filters, so that the error report indicates which filter the error occurs in, e.g., ``` PF = FilterRules(list(regionFilter = regionFilter)) ``` Alternatively, you could try to evaluate `traceback()` a ...
written 12 days ago by Martin Morgan ♦♦ 23k
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Answer: A: BiocManager upgrade problem
... Likely what you have done is updated your R but reused your installed packages library. A better strategy is to make sure that the `.libPaths()` are unique to each version of R + Bioconductor; discussed a bit ironically in the BiocManager [vignette][1]. To continue down the path that you're on, in ...
written 12 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Great; for a little context, if the package (like affycoretools) does not contain C-level (or Fortran or C++) source code, then R can install the package 'from source' without additional tools. On the other hand, if there is C source code, then R needs access to a correctly configured compiler tool ...
written 12 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... What happens when you answer 'no' to the question about installing from source? ...
written 13 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... It is a one-click download https://cran.r-project.org/bin/macosx/ plus a couple more clicks to install... Your packages will need to be updated ``` install.packages("BiocManager") BiocManager::install(version = "devel") BiocManager::valid() ``` ...
written 13 days ago by Martin Morgan ♦♦ 23k
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Comment: C: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... If you're wanting to use the devel version of Bioconductor, then indicate that with BiocManager BiocManager::install(version="devel") and then re-run `BiocManager::valid()` -- it will indicate that there are a few packages that are out-of-date, and you should then update them. If you're wanti ...
written 17 days ago by Martin Morgan ♦♦ 23k
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Comment: C: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... I guess BiocManager::valid() is almost as displeased as before; use BiocManager rather than github to manage your installations. The solution used here, to install Bioconductor packages from github, is not recommended at all. ...
written 17 days ago by Martin Morgan ♦♦ 23k
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Answer: A: GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
... Likely you have mixed release (even numbered version 'y' in x.y.z) and devel (odd numbered y) versions of packages. What does BiocManager::valid() report? The BiocManager vignette has information about maintaining different releases. ...
written 17 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Scholar 11 weeks ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Scholar 11 weeks ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Popular Question 9 months ago, created a question with more than 1,000 views. For BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
Scholar 9 months ago, created an answer that has been accepted. For A: bplapply with ShortRead functions
Appreciated 9 months ago, created a post with more than 5 votes. For Bioconductor Technical Advisory Board
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: RSVSim insertions from chr1 to chr2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rsamtools use for R version 3.4.1
Scholar 9 months ago, created an answer that has been accepted. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Best alternative annotation package to BiomaRt
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioconductor Senior Programmer / Analyst
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: how does coverage() works
Scholar 9 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 9 months ago, created an answer that has been accepted. For A: Ranges from a fasta file
Scholar 9 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Scholar 9 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Appreciated 9 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 9 months ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Scholar 9 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 9 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 9 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

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