Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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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 ...
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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 5 weeks 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 6 weeks 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 weeks ago by Vincent J. Carey, Jr.6.2k • updated 10 weeks ago by Martin Morgan ♦♦ 21k
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Comment: C: Cannot load CEL files
... does file.exists("~/Downloads/GSE17204_RAW/GSM430339.CEL") yield TRUE? ...
written 4 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs
... This was cross-posted to bioc-devel.  The answer that I provided there was: You can get the information through the merged tables: > dbListTables(con) [1] "gds" "gds_subset" "geoConvert" [4] "geodb_column_desc" "gpl" "gse" [7] "gse_gpl ...
written 4 months ago by Vincent J. Carey, Jr.6.2k • updated 4 months ago by Sean Davis21k
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Answer: A: how to find Snps that are within 1e6 from gene
... You should structure the location data you've provided as GRanges instance. if your gene data are available in a data.frame as e.g.,  > genes geneName chrom txStart txEnd 1 A1BG chr19 58858171 58864865 2 A1BG-AS1 chr19 58863335 58866549 3 A1CF chr10 52559168 52645435 ...
written 7 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Mapping regions to gene symbols
... look for the difference between seqinfo(mygr) and seqinfo(r2syms) seqlevelsStyle(mygr) and seqlevelsStyle(r2syms) get them to coincide. it can take some work. simplest is often seqlevelsStyle(mygr) = seqlevelsStyle(r2syms) assuming GenomeInfoDb package is attached On Sat, Jul 1, 2017 at 3:2 ...
written 7 months ago by Vincent J. Carey, Jr.6.2k
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Answer: A: Mapping regions to gene symbols
... For all its apparent simplicity, this question is not very clear.  One warning sign is: seqinfo: 23 sequences from an unspecified genome; no seqlengths How are we supposed to know what reference genome defines the genomic coordinates?  This is essential information for mapping between characteris ...
written 7 months ago by Vincent J. Carey, Jr.6.2k
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Comment: C: No annotation for single SNPs
... i'd say the clue is to look at the output of AllVariants() maybe Val can comment further on how to increase scope On Wed, Jun 21, 2017 at 7:48 AM Lna [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Lna <htt ...
written 8 months ago by Vincent J. Carey, Jr.6.2k

Latest awards to Vincent J. Carey, Jr.

Scholar 22 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 23 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 2.3 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 3.5 years ago, created 100 posts.

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