Moderator: jared.andrews07

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jared.andrews078.3k
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Bioinformatics Research Scientist at St. Jude Children's Research Hospital studying pediatric brain tumors. Ph.D. at Washington University in St. Louis performing comparative multi-omics studies on B and T cell lymphomas to identify their epigenetic underpinnings. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user, fledgling R developer, hater of Perl. 

Posts by jared.andrews07

<prev • 924 results • page 1 of 93 • next >
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Comment: C: scRNA-seq analysis of two data-sets
... > Why is it better to avoid integration as a whole? It is generally a pain and can sometimes obfuscate truly unique populations by smacking them together. It's not a perfect process, though improvements have been made since I initially posted this. As well as benchmarking studies that show which ...
written 1 day ago by jared.andrews078.3k
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Comment: C: Best practice to integrate OMIM data into bioinformation analysis pipeline
... This is too broad to answer. Integrate how? What information do you want? What is your query? Regardless, you'll have to register for either API or download access first. I'd probably use the [API](https://www.omim.org/help/api) for low volume stuff, but if you're going to end up making a million r ...
written 4 days ago by jared.andrews078.3k
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Comment: C: scRNA Cell Type ID web resources
... You can certainly submit a PR to `celldex` with your dataset and it will get added, though we tend to pull the data directly from a hosted source (e.g. GEO). You can also check the [scRNAseq](https://bioconductor.org/packages/release/data/experiment/html/scRNAseq.html) data package, which has severa ...
written 4 days ago by jared.andrews078.3k
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Comment: C: Annotating peaks with genes
... The [ChIPseeker](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) R package will also assign peaks to genes (and provides some viz functions, etc) if you need other alternatives. ...
written 4 days ago by jared.andrews078.3k
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Answer: A: recent Hi-C databases
... [This list](https://github.com/mdozmorov/HiC_data) on github is a pretty good one in terms of datasets/resources. [3DIV](http://kobic.kr/3div/) might be a little more what you're after though. ...
written 8 days ago by jared.andrews078.3k
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Comment: C: How to make a complicated dot plot for scRNAseq marker genes with ggplot2?
... What do you mean exactly? I can tell you now that the cell numbers in each cluster are best added after the fact in Illustrator or your favorite figure editor. Getting the clusters labeled and oriented as in that figure would be something like: ``` dittoDotPlot( myRNA, c("gene1", "gene2", "gene ...
written 8 days ago by jared.andrews078.3k
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Comment: C: How to make a complicated dot plot for scRNAseq marker genes with ggplot2?
... That it does, if you're using Seurat. I like to think the dittoSeq version is more flexible given it handles metadata variables and multiple data formats, but I was involved in its development so I am a bit biased. ...
written 8 days ago by jared.andrews078.3k
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Comment: C: How to make a complicated dot plot for scRNAseq marker genes with ggplot2?
... How so? Harmony has no viz functions. ...
written 9 days ago by jared.andrews078.3k
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Answer: A: Normalization before or after merging the samples in Seurat
... Example code would be helpful, but generally you merge samples before doing anything else. Doing QC prior to merging is fine, since you should be doing that on a sample by sample basis anyway. I'd recommend taking a look at the [Seurat vignette on using it with harmony](https://htmlpreview.github.i ...
written 9 days ago by jared.andrews078.3k
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Answer: A: How to make a complicated dot plot for scRNAseq marker genes with ggplot2?
... Use `dittoDotPlot` from the [dittoSeq](https://bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html#561_dittoDotPlot) package. Much easier than from scratch. The resulting plot is still a ggplot2 object, so you can customize as you'd like. Though the function itself is al ...
written 9 days ago by jared.andrews078.3k

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