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Moderator: Vincent J. Carey, Jr.

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Email:
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Posts by Vincent J. Carey, Jr.

<prev • 661 results • page 1 of 67 • next >
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Bioconductor and WGS: recommended practices?
... I searched the support site for references to WGS, and "whole genome sequencing", and nothing came back. One experimental data package called cgdv17 is available that includes excerpts from Complete Genomics public release. This package was apparently made back in 2011. It defines a "raggedVariant ...
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Comment: C: error in makeTxDbFromUCSC
... I have had a look at this, and certainly confirm the error event with devel branch. A similar error occurs with the request for refGene with hg38. Browse[6]> where where 1: .check_foreign_key(transcripts_tx_chrom, NA, "transcripts$tx_chrom", chrominfo$chrom, NA, "chrominfo$chrom ...
written 27 days ago by Vincent J. Carey, Jr.6.3k
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Comment: C: connection to stringdb database server failed
... I can confirm this with the current version in devel branch.  There may be an issue with the URL generated in the call to plot_network.  I conjecture this because the api seems to work when used directly ... e.g., with https://string-db.org/api/image/network?identifiers=TP53%0dEGFR&add_white_nod ...
written 7 weeks ago by Vincent J. Carey, Jr.6.3k
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Job: Software ecosystem architect position, Dana Farber Cancer Institute
... https://careers-dfci.icims.com/jobs/12755/research-scientist/job Overview Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer ...
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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 4 months ago by Vincent J. Carey, Jr.6.3k
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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 6 months ago by Vincent J. Carey, Jr.6.3k
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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 6 months ago by Vincent J. Carey, Jr.6.3k
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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 6 months ago by Vincent J. Carey, Jr.6.3k
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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 9 months ago by Vincent J. Carey, Jr.6.3k
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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 12 months ago by Vincent J. Carey, Jr.6.3k

Latest awards to Vincent J. Carey, Jr.

Appreciated 20 months ago, created a post with more than 5 votes. For edX online course introducing Bioconductor now up and running
Scholar 2.8 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 3.0 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 3.3 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 4.5 years ago, created 100 posts.

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