Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Comment: C: Using AMI with StarCluster - error authenticating
... We are finding that cfncluster creation of clusters in EC2 is extremely slow, relative to the solution available a few years through starcluster.  Any other approaches in use in our community? ...
written 9 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
... I don't know that SummarizedExperiment is a good target for what you are trying to do. Is there a matrix of values to serve as "assay", with rows corresponding to features and columns corresponding to samples? Organizing such a matrix in coordination with feature-level and sample-level and experime ...
written 10 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
...   Briefly, there is no simple approach to this.  However, to get a working example: library(GenomicRanges) library(SummarizedExperiment) example(GRangesList) # creates 'grl' in .GlobalEnv colrep = function(x,n) matrix(x, nr=length(x), nc=n) # utility to create usable 'assay' msel = lapply(grl, ...
written 10 weeks ago by Vincent J. Carey, Jr.6.1k
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Comment: C: "developing" with HDF5Array
... benchOOM now has getLitGeu() which restores a saved HDF5-backed SummarizedExperiment that is stored in the package ...
written 3 months ago by Vincent J. Carey, Jr.6.1k
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Comment: C: "developing" with HDF5Array
... Excellent.  Thanks very much. ...
written 3 months ago by Vincent J. Carey, Jr.6.1k
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Comment: C: "developing" with HDF5Array
... benchOOM has been updated to include rhconvert, which converts the assay portion of a RangedSummarizedExperiment to HDF5Array (delayed) and returns a SummarizedExperiment with this alternate representation of the assay data.  (rhconvert = "RangedSummarizedExperiment to HDF5 conversion") ...
written 3 months ago by Vincent J. Carey, Jr.6.1k
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Answer: A: "developing" with HDF5Array
... Thanks Hervé.  I am not considering the cases of mixed assay representation, or even multiple assays.  At the moment I am trying to get some realistic performance appraisals of the simple hybrid situation: single large assay in HDF5, everything else in the standard RAM-based representation.   I agre ...
written 3 months ago by Vincent J. Carey, Jr.6.1k
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Tutorial: "developing" with HDF5Array
... I'd like to get some statistics on performance and maintenance issues of using the delayed HDF5 back end for SummarizedExperiments.  This is part of a general project started in the benchOOM package.  In that package I tentatively defined a generic "writeHDF5Dataset" and a method for RangedSummarize ...
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Extension to GoogleGenomics: getVariantCalls
... We have introduced a function, getVariantCalls, into GoogleGenomics, that has the same interface as getVariants, but returns a VRanges with genotype content for all samples. The function has only been tested against the 1000 genomes variant datasets, and at present does not acquire call-related i ...
genetics googlegenomics variants written 3 months ago by Vincent J. Carey, Jr.6.1k
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Comment: C: VariantAnnotation error with readVcf after genotypeToSnpMatrix
... I can't reproduce on several platforms.  Some of your packages seem out of date.  Use library(BiocInstaller); biocValid() and update to a consistent state.  I don't see VariantAnnotation version in your sessionInfo() above. ...
written 6 months ago by Vincent J. Carey, Jr.6.1k

Latest awards to Vincent J. Carey, Jr.

Scholar 13 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Scholar 14 months ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: how can I install packages in docker/R/bioconductor so that they persist?
Centurion 2.8 years ago, created 100 posts.

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