User: gaiusjaugustus

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University of Arizona
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http://icers.arizona.edu/
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gaiusdivifilius
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Posts by gaiusjaugustus

<prev • 14 results • page 1 of 2 • next >
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Split Genomic Ranges With Reference Overlaps (Centromere)
... Hi, I have list of ranges (that I can convert to a genomic ranges object), some of which pass over the centromere of a chromosome.  I also have a file that denotes the start and end of each chromosome arm (leaving out the centromere). For example: Chromosome   Start     End     A ...
genomicranges granges split written 6 months ago by gaiusjaugustus0 • updated 6 months ago by koisingh690
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TCGAbiolinks query error
... I am trying to get a list of samples that have certain datasets.  My goal is to use TCGAbiolinks to query the database and then will compare queries from different data types (e.g. Mutation, RNAseq, and Methylation450).  This will allow me to identify cases that have multiple data types and only dow ...
tcgabiolinks written 9 months ago by gaiusjaugustus0
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RnBeads, enrichment analysis
... Hi, I have completed my first DMR analysis with the 450k array data using RnBeads.  The final differential analysis line of code was: rnb.run.differential(rnb.set, report.dir) But an enrichment analysis wasn't run.  Here are my options. rnb.options(filtering.sex.chromosomes.removal=TRUE, identifi ...
rnbeads written 13 months ago by gaiusjaugustus0
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Comment: A: Create VRanges object from mutation data (txt extracted from annotated vcf)
... In order to fix this, I had to convert my original dataframe to a GRanges object.  Then I had to input some fields as GRanges objects and some from the original text file.   VRanges(     seqnames = seqnames(CCCC_GRanges),     ranges = ranges(CCCC_GRanges),     ref = CCCC_muts$Reference_Allele,    ...
written 13 months ago by gaiusjaugustus0
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Create VRanges object from mutation data (txt extracted from annotated vcf)
... I am working on using the SomaticSignatures package on a list of mutations I've received from a collaborator.  The file has all the variants listed in a tab-delimited text file, with all the fields you would expect from an annotated vcf file (e.g. Chromosome, Start_Position, End_Position, Reference_ ...
variantannotation iranges written 13 months ago by gaiusjaugustus0 • updated 13 months ago by Michael Lawrence9.8k
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Comment: C: biocLite installs older version of SummarizedExperiment package
... Thank you.  Following the instructions on the bioconductor troubleshooting page fixed the issue. ...
written 14 months ago by gaiusjaugustus0
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Comment: C: biocLite installs older version of SummarizedExperiment package
... C:\Program Files\R\R-3.3.1\bin>R.exe --vanilla R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it ...
written 14 months ago by gaiusjaugustus0
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Comment: C: biocLite installs older version of SummarizedExperiment package
... Sorry, meant to mention that I checked my R version. I'm running 3.3.1.  And I have Bioconductor 3.2. ...
written 14 months ago by gaiusjaugustus0
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biocLite installs older version of SummarizedExperiment package
... Hi, Trying to install TCGAbiolinks, which has version 1.2.3 of SummarizedExperiments.  When I install via biocLite(), I get version 1.0.2.  I tried checking out the Github repo, but didn't see any more information there. I also tried removing the package and reinstalling it, with no improvement. ...
summarizedexperiment written 14 months ago by gaiusjaugustus0
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Howto: View Pileup or Base level stats in R using Rsamtools or rbamtools
... Hello, I have 50 bam files that I'd like to go through.  I have a list of mutations in 21 genes in those bamfiles, and I'd like to write some code to go through each gene, locate the base that is mutated, and get a readout of what's there in the tumor sample and the normal sample. In the past I've ...
rsamtools rbamtools written 14 months ago by gaiusjaugustus0 • updated 14 months ago by li lilingdu450

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