Moderator: jared.andrews07

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jared.andrews077.6k
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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 • 846 results • page 1 of 85 • next >
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Comment: C: Mitochondrial genes in single cell nuclear RNAseq data
... Variable mitochondrial genes are pretty typical, and as genomax said, this could be indicative of contamination (either through intact cells or ambient RNA). What % of reads are in mitochondrial genes? If it's only a few percent, you can likely ignore them. ...
written 1 day ago by jared.andrews077.6k
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Comment: C: How to make a PCA plot in three dimensional-RNA-Seq analysis
... This has been discussed several times on Biostars and elsewhere. Several answers [here](https://www.biostars.org/p/333436/) that will be helpful for you. ...
written 1 day ago by jared.andrews077.6k
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Comment: C: Is it possible to estimate the proportion of contamination from GC contents ?
... As genomax mentioned, no, you are not going to be able to determine this from GC content. If you have a large proportion of reads that don't map to the genome of your target organism, there are a few methods you could try. ...
written 2 days ago by jared.andrews077.6k
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Comment: C: Is it possible to estimate the proportion of contamination from GC contents ?
... What do you mean by "a significant GC content plot"? ...
written 3 days ago by jared.andrews077.6k
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Answer: A: Removing RBC contamination in Seurat
... Sure. Just remove the clusters that have those as markers, though be warned that certain vascular/endothelial cell populations may have them as markers as well. Typically, RBCs cluster well on their own, so removing them is pretty simple. See `?SubsetData` or check out the [Seurat cheatsheet](https: ...
written 3 days ago by jared.andrews077.6k
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Comment: C: Cross-specie Integration Using Seurat
... How can you expect them to find anchors if you don't use common gene names? Integration requires the comparison of common features. In this case, that'd be orthologous gene. So save your current gene names somewhere in the metadata, convert one species' orthologous genes to the other or vice versa, ...
written 3 days ago by jared.andrews077.6k
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Comment: C: R - How to convert a sequence in a fasta file into a matrix
... Do you *have* to use a matrix of individual characters? Seems simpler to just use a list or vector of hexamers - it likely wouldn't require much of a change to your scoring function. If you're dead set on splitting the hexamers, take a look at the [strsplit](https://stat.ethz.ch/R-manual/R-devel/l ...
written 3 days ago by jared.andrews077.6k
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Comment: C: Biorad/ddseq scATACseq fragements.tsv.gz integration
... I see you did so [here](https://github.com/GreenleafLab/ArchR/issues/366) and got a useful response to get things working. Linking here so other users may find it as well. ...
written 3 days ago by jared.andrews077.6k
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Comment: C: R - How to convert a sequence in a fasta file into a matrix
... That's great! But we need to *see* that effort. Show us what you've tried and the specific issue(s) you're running into. This also has the benefit of forcing you to document what you've done and generate a reproducible example (which you've already done in this case, so kudos). In this process, you' ...
written 3 days ago by jared.andrews077.6k
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Comment: C: R: Plotting MSMC/PSMC results using ggplot2
... You're likely to get more help if you post your own question. Piggybacking on another one makes it tough for other users to find your question. ...
written 4 days ago by jared.andrews077.6k

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