User: jrleary

gravatar for jrleary
jrleary170
Reputation:
170
Status:
Trusted
Location:
Lineberger Comprehensive Cancer Center
Last seen:
3 weeks, 4 days ago
Joined:
1 year, 2 months 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 • 63 results • page 4 of 7 • next >
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170
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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 11 months ago by jrleary170 • updated 11 months ago by jared.andrews078.3k
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Comment: C: Recommendations for Whole Genome Sequencing Workflow
... Ah ok. Thank you for the clarification. ...
written 11 months ago by jrleary170
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Comment: C: Recommendations for Whole Genome Sequencing Workflow
... Are either of GATK or SpeedSeq capable of analyzing the microbiome of a sample? I should have clarified in my original post that that's what we're primarily interested in. ...
written 11 months ago by jrleary170
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Recommendations for Whole Genome Sequencing Workflow
... My lab is looking to get into Whole Genome Sequencing, and we of course need a processing and analysis pipeline for the data we generate. I've been reading up on WGS / WES, and I understand the basics but I haven't seen any "best practices" type documents / tutorials like those that exist for single ...
genome wgs assembly written 11 months ago by jrleary170 • updated 11 months ago by bruce.moran860

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Popular Question 6 months ago, created a question with more than 1,000 views. For Should I Run Clustering on PCA or t-SNE Components?
Supporter 10 months ago, voted at least 25 times.
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.

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