User: jared.andrews07

gravatar for jared.andrews07
jared.andrews074.3k
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Location:
St. Louis, MO
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https://github.com/j-a...
Last seen:
13 hours ago
Joined:
2 years, 6 months ago
Email:
j**************@gmail.com

Ph.D. candidate at Washington University in St. Louis. 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 developer, hater of Perl. 

Posts by jared.andrews07

<prev • 543 results • page 1 of 55 • next >
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Answer: A: Looking for the soft that generated this figure
... They're just Venn Diagrams. You can create them with [venn](https://cran.r-project.org/web/packages/venn/venn.pdf) or many other packages. ...
written 18 hours ago by jared.andrews074.3k • updated 17 hours ago by RamRS25k
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Answer: A: How to use SingleR for annotating single-cell transcriptomics dataset with our o
... Sure, you just have to feed it the counts (`ref` argument) and a vector of labels (`labels` argument) corresponding to each sample. Reading `?SingleR` should explain pretty clearly. ...
written 23 hours ago by jared.andrews074.3k
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Comment: C: CNV Profile figure
... Have you done QC on the WES data? This looks like a potential quality issue. ...
written 2 days ago by jared.andrews074.3k
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Comment: C: CNV Profile figure
... Agreed, this looks crazy messy. What sort of data is this? Exome, wgs? I've never used Control-FREEC, but it doesn't look like segmentation is being performed either. ...
written 4 days ago by jared.andrews074.3k
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Answer: A: CNV calling for haplotype reference genome
... [CNVkit](https://cnvkit.readthedocs.io/en/stable/quickstart.html) should work, though it does require a normal "reference" sample(s) to base things on. ...
written 4 days ago by jared.andrews074.3k
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Answer: A: SEURAT scRNA-seq and library contribution for each cluster
... I prefer [dittoSeq](https://github.com/dtm2451/dittoSeq) for tasks like this. It works on Seurat objects directly and has much better visualizations than Seurat. Should be included in the next Bioconductor release. With dittoSeq, this would be done with: ``` dittoBarPlot("your_cluster_column", you ...
written 5 days ago by jared.andrews074.3k
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Comment: C: Down regulated genes in sC-RANseq
... You certainly can, people just tend to show those upregulated in a given cell-type/cluster, as it's arguably easier to interpret. ...
written 9 days ago by jared.andrews074.3k
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Comment: C: Enhanced Volcano removal of labels
... Can probably just use `selectLab = c()`, but haven't tested it. ...
written 11 days ago by jared.andrews074.3k
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Comment: C: Feature Selection in 10X scRNA-seq data
... Think it also depends on sample. Normal PBMCs are fairly consistent between samples without batch correction through standard pipelines, assuming they're done fairly close to each other by the same person. Disease samples are a different story though. ...
written 13 days ago by jared.andrews074.3k
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Comment: C: Feature Selection in 10X scRNA-seq data
... My expectation is that you'd see fairly significant sample-to-sample effects with zero normalization, but would be interested in seeing if that's actually true. ...
written 14 days ago by jared.andrews074.3k

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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How to choose good tools for identifying functional SNPs?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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