User: jrleary

gravatar for jrleary
jrleary130
Reputation:
130
Status:
Trusted
Location:
Lineberger Comprehensive Cancer Center
Last seen:
4 months, 3 weeks ago
Joined:
1 year 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 • 61 results • page 3 of 7 • next >
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Picard CollectSequencingArtifactMetrics error
... I'm analyzing whole exam sequencing data, and using Picard to perform some QC on my aligned / sorted / duplicated removed .bam files. When running `picard CollectSequencingArtifactMetrics`, I receive the following error: ``` Exception in thread "main" picard.PicardException: Record contains library ...
picard wes written 6 months ago by jrleary130
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Comment: C: Coloring single cell dimension-reduced plots in R, which palettes can handle hig
... Ah, I didn't think about `grDevices`. Thank you! ...
written 6 months ago by jrleary130
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Coloring single cell dimension-reduced plots in R, which palettes can handle high n?
... I'm looking to use something different than the built-in color palettes in `Seurat`, but I'm finding it very difficult to find packages that can handle 20+ discrete colors. I've looked through `RColorBrewer` and `colorspace`, as well as `ggsci`, and all max out around 12 colors from what I can see. ...
R ggplot2 written 6 months ago by jrleary130
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Comment: C: Where to find reference transcriptome for firefly?
... Awesome, thanks so much! ...
written 6 months ago by jrleary130
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Where to find reference transcriptome for firefly?
... I'm not sure if this exists (never worked with any genomes outside human/mouse before), but if possible I need to download a reference transcriptome for a firefly, specifically *Photinus pyralis*. The transcriptome would need to work with `cellranger`, i.e. I would need to be able to align some FAST ...
scrna-seq alignment cellranger transcriptome written 6 months ago by jrleary130 • updated 6 months ago by genomax92k
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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 8 months ago by jrleary130
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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 8 months ago by jrleary130 • updated 8 months 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 8 months ago by jrleary130
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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 9 months ago by jrleary130
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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 9 months ago by jrleary130

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Supporter 8 months ago, voted at least 25 times.
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.

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