User: jrleary

gravatar for jrleary
jrleary70
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70
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Location:
Lineberger Comprehensive Cancer Center
Last seen:
3 days, 12 hours ago
Joined:
4 months, 1 week ago
Email:
j******@live.unc.edu

Lowly undergrad research assistant running bulk / single cell RNAseq and downstream analysis. Focused on pancreatic cancer. 

Posts by jrleary

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Papers on Paired Single Cell and Bulk RNAseq
... Is [this the presentation][1] to which you are referring? I can't find any UW videos with Dr. Shalek that are recent. [1]: https://www.youtube.com/watch?v=2-N3SPPHt6o ...
written 4 days ago by jrleary70
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Papers on Paired Single Cell and Bulk RNAseq
... My lab has paired bulk and single cell RNAseq for several tumor samples. We'd like to somehow use our single cell results (basically annotated clusters of cells w/ cell identities and differentially expressed genes, plus a malignant / normal cell label) to inform our bulk RNAseq analysis, but I'm so ...
scrna-seq rna-seq written 5 days ago by jrleary70 • updated 5 days ago by atgustin10
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Comment: C: Identifying tumor cells in single cell RNAseq data
... Just an update for future readers: I've had decent success replicating CNV analyses with `CONICSmat` on publicly available PDAC scRNA-seq data. Obviously processing, filtering, normalization, etc. methods are going to differ between labs but I've been able to see the strongest amplifications and del ...
written 24 days ago by jrleary70
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Comment: C: Identifying tumor cells in single cell RNAseq data
... The data we're analyzing is from PDAC, so I'll be doing some pancreas-specific research. Are there any other extant computational methods you'd recommend for differentiating between malignant and normal? ...
written 5 weeks ago by jrleary70
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Comment: C: Identifying tumor cells in single cell RNAseq data
... I'll see what I can do, but I believe at the moment we only have scRNA data, maybe some paired bulk RNAseq data. With those resources, do you think trying to estimate CNVs is worth the time or would it be too noisy? ...
written 5 weeks ago by jrleary70
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Comment: C: Identifying tumor cells in single cell RNAseq data
... Thank you both. I had been using the Patel paper as a reference but it looks like I'm going to have to do a much deeper dive research-wise before I start analyzing anything. I don't want to be lacking in domain knowledge. ...
written 5 weeks ago by jrleary70
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Comment: C: Identifying tumor cells in single cell RNAseq data
... That thread of yours is where I found `CONICSmat` in the first place :) With regards to using CNVs to identify tumor cells, are there any best-practices documents / guides floating around? I come from a pure stats background so I'm less familiar with some of the (to me) more complicated biology conc ...
written 5 weeks ago by jrleary70
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Answer: A: Marker genes for different cell types
... In my opinion annotating cell clusters using marker genes by hand is a massive pain and is very subjective. I used the [SingleR package][1], which iteratively compares non-parametric gene expression profile correlations of your cells with annotated reference cells. It's very easy to set up and use a ...
written 5 weeks ago by jrleary70
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Comment: C: Identifying tumor cells in single cell RNAseq data
... I think I'll be giving `CONICSmat` a go as a method of identifying CNVs / tumor cells. Thanks for the input. ...
written 5 weeks ago by jrleary70
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Identifying tumor cells in single cell RNAseq data
... My lab does a lot of single cell RNAseq of samples that include tumor cells. I have a pipeline in place that reduces dimension, clusters cells, and automatically assigns cell type labels to those clusters (mostly using `Seurat` and `SingleR`). However, I do not currently have a way to differentiate ...
R scrnaseq cancer written 5 weeks ago by jrleary70 • updated 5 weeks ago by jared.andrews075.3k

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