Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Comment: C: Data from ##SAMPLE lines in VCF?
... I can confirm this.  None of our example VCF in VariantAnnotation use the META header record type (https://samtools.github.io/hts-specs/VCFv4.3.pdf section 1.4.8).  Additionally writeVcf-methods.Rd mentions Bioconductor 3.1 and the contemporaneous standard v4.2 of VCF spec.  It looks like there is ...
written 20 days ago by Vincent J. Carey, Jr.6.2k
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Comment: C: VariantAnnotation error with readVcf after genotypeToSnpMatrix
... please supply sessionInfo() result. The installation path suggests R 3.3 is in use, which is out of date. I find that example(readVcf) works fine on an up to date installation. You need to use biocValid() with BiocInstaller, or really update your system, use BiocManager, and supply a reproducible ...
written 8 weeks ago by Vincent J. Carey, Jr.6.2k
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... > install("sesameData", localHub=TRUE) # succeeded with the following sessionInfo, but took a long time at "testing if installed package can be loaded" > sessionInfo() R version 3.5.1 Patched (2018-07-21 r74998) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12 ...
written 9 weeks ago by Vincent J. Carey, Jr.6.2k
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bug found in restfulSE::BQ3_Array/repaired
... A problem was identified with the BQ3_Array function in restfulSE.  BigQuery results were mislabeled.  This affects the results of pancan_SE in release and devel. A corrected version of the package is available in https://github.com/vjcitn/restfulSE/tree/vjcRepair After additional testing the cor ...
bug written 10 weeks ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Recommendations for Protein Network Data Structure
... is the infrastructure in ppiStats package relevant?  graph package seems pretty relevant, you can annotate nodes and edges very generally. ...
written 5 months ago by Vincent J. Carey, Jr.6.2k
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Job: Postdoctoral position at Harvard Medical School
... Postdoctoral Position in Bioinformatics Channing Division of Network Medicine Brigham and Women’s Hospital and Harvard Medical School   The Channing Division of Network Medicine, Brigham and Women’s Hospital, and Harvard Medical School are seeking applicants for a postdoctoral position in bioinf ...
job bioinformatics postdoctoral fellow written 8 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: How to download TCGA vcf file from GDC data portal?
... See https://wiki.nci.nih.gov/display/TCGA/Access+Tiers This indicates that the VCF are controlled access and thus you would only get them through some authentication process with NCI. ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: seqlevels(param) not in BAM header
... I can't tell what package/command you are using.  It seems to me you need to look carefully at the 'param' in use. ...
written 9 months ago by Vincent J. Carey, Jr.6.2k
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News: edX online course introducing Bioconductor now up and running
... A new edition of the Introduction to Bioconductor in the edx series on Data Analysis for the Life Sciences has been released.  Visit https://www.edx.org/course/introduction-bioconductor-annotation-harvardx-ph525-5x-0 for more information.  The curriculum covers chapters 11-13 of the online text "B ...
annotation news bioconductor written 10 months ago by Vincent J. Carey, Jr.6.2k • updated 10 months ago by Martin Morgan ♦♦ 22k
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Comment: C: Cannot load CEL files
... does file.exists("~/Downloads/GSE17204_RAW/GSM430339.CEL") yield TRUE? ...
written 11 months ago by Vincent J. Carey, Jr.6.2k

Latest awards to Vincent J. Carey, Jr.

Appreciated 15 months ago, created a post with more than 5 votes. For edX online course introducing Bioconductor now up and running
Scholar 2.5 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 2.9 years 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 4.2 years ago, created 100 posts.

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