Moderator: Obi Griffith

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Obi Griffith16k
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Washington University, St Louis, USA
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http://www.obigriffith...
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obigriffith
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I am an Assistant Professor of Medicine (Oncology) and Genetics at Washington University School of Medicine and Assistant Director at the McDonnell Genome Institute. I study cancer genomics, primarily through clinical statistics and bioinformatic analyses of next-generation sequence data such as whole genome (WGS), exome, and transcriptome (RNA-seq) data.

Posts by Obi Griffith

<prev • 418 results • page 2 of 42 • next >
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Comment: C: Plotting numbers of somatic substitutions per megabase (MB)
... Are you supplying the Alexandrov example just to demonstrate layout? I ask because this figure has a lot more going on than just mutations/MB. It is showing mutations/MB brokend down by mutation type in several different ways. If that is what you want then it is a complicated question/answer. ...
written 15 months ago by Obi Griffith16k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... Yes. Just look at the format of the "mutation_data" object. If you can add another column with VAF values then you should be able to just specify mainLabelCol="X" where X is the name of your new VAF column rather instead of "amino.acid.change". ...
written 16 months ago by Obi Griffith16k
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... I'm not sure what you are asking. Do you mean the variant allele frequency for each gene/sample? As a text value in each cell? Or, something else? ...
written 16 months ago by Obi Griffith16k
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Comment: C: Announcing new Bioinformatics Workshops in NYC: Apr 27 - May 3, 2015
... Hello Obi Griffith! We believe that this post does not fit the main topic of this site. Old workshop now outdated. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a repl ...
written 16 months ago by Obi Griffith16k
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Comment: C: How to create a mutation lolliplot with GenVisR
... Perhaps @zlskidmore could comment. ...
written 20 months ago by Obi Griffith16k
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Answer: A: TCR Sequencing Lack of Repertoire Overlap
... Another formal possibility is that your mice are not as isogenic as you think. I have had several experiences where we were operating on the assumption that highly inbred lab mouse strains are "genetically identical" but in fact upon whole genome sequencing determine that substantial genetic diversi ...
written 22 months ago by Obi Griffith16k
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Comment: C: Cost Comparison Between Microarray And Rna-Seq Experiment
... This answer is now quite out of date with respect to RNAseq costs. These still vary widely depending on the protocol, target number of reads, etc. However to update the ballpark numbers I estimate that a typical RNA experiment starting from isolated RNA (including sample management, Illumina TruSeq ...
written 22 months ago by Obi Griffith16k
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... You can set dendrogram="none" to stop drawing the dendrograms. To stop actual clustering you can set Rowv=FALSE and/or Colv=FALSE depending on which dimension(s) you don't want clustering for. If you turn off both, you could also drop the hclustfun and distfun parameters since these will have no use ...
written 22 months ago by Obi Griffith16k
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Tool: GenVisR: Genomic Visualizations in R
... Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging. "Genomic Visualizations in R" (GenVisR) attempts to alleviate this burden by providing highly customizable publication-quality graphics supporting multiple species and focused primari ...
genomic visualization genvisr rna-seq tool written 22 months ago by Obi Griffith16k
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Tutorial: How to create a mutation lolliplot with GenVisR
... This tutorial makes use of the GenVisR package. Please cite: Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print] PubMed | Bioinformatics Journal | BioRxiv | Bioconductor | ...
graphics bioconductor tutorial R genvisr written 22 months ago by Obi Griffith16k • updated 20 months ago by mia12600

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Good Answer 16 days ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
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