User: jrleary

gravatar for jrleary
jrleary130
Reputation:
130
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Location:
Lineberger Comprehensive Cancer Center
Last seen:
2 months, 2 weeks ago
Joined:
10 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 • 61 results • page 1 of 7 • next >
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Comment: C: Estimating hetero/homogeneity of scRNAseq clusters
... Sorry, this is a bit confusing to me. Are you saying that any genes I used to define cell subtypes must be surface proteins? I'm not attempting to define novel cell subtypes, just identify already existing ones within my samples. ...
written 3 months ago by jrleary130
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Comment: C: Estimating hetero/homogeneity of scRNAseq clusters
... Yes, I do assign clusters cell labels based on manual marker gene investigation as well as automatic comparison w/ reference data using `SingleR`. I'm looking for a metric I can used to measure how similar the cells within a cluster are to each other, so that I can give myself an idea of which clust ...
written 3 months ago by jrleary130
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Estimating hetero/homogeneity of scRNAseq clusters
... I'm working on some downstream analysis of some single cell samples, and I'm trying to decide which clusters are worth investigating further to see if they contain subtypes. Is there a method similar to Intra-class Correlation Coefficient from sample design theory that I could use to determine which ...
scrna-seq R written 3 months ago by jrleary130 • updated 7 weeks ago by Biostar ♦♦ 20
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What are the differences between the Seurat v3 clustering algorithms?
... I'm trying to decide which of the default `Seurat v3` clustering algorithms is the most effective. The 3 R-based options are: 1)Louvain, 2) Louvain w/ multilevel refinement, and 3) SLM. The documentation is very vague about what the differences between the algorithms are, and gives no hint as to whi ...
scrna-seq R seurat written 3 months ago by jrleary130
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Comment: C: Cell type pathway ScRNAseq
... Along the other suggestions, I'll add the `VAM` package implemented in this preprint: [Variance-adjusted Mahalanobis: a fast and accurate method for cell-specific gene scoring][1]. I don't think the package is up on GitHub / CRAN yet, but if you contact the author he's happy to share the compiled `. ...
written 3 months ago by jrleary130
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Comment: C: How to get same reproducible value in R?
... Reading through the `BMIQ.R` file, it looks to me that the programmers invoke `set.seed` before any of the function calls that involve stochasticity, so I think it should be handled. I'm not entirely sure what's going on as I can't run your code myself, but it could be an issue with how R rounds num ...
written 3 months ago by jrleary130
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Comment: C: Using R Studio on Cloud
... You can render `.Rmd` files on your university's HPC. I create the `.Rmd` file locally, and send it to the cluster. I have a script there called `render.R` that looks like this: ``` rmarkdown::render("path/to/uploaded/file.Rmd") ``` I then submit a job calling that script (my uni uses `slurm`, you ...
written 3 months ago by jrleary130
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Answer: A: How to get same reproducible value in R?
... Looking at the `champ.norm` documentation on Bioconductor, the function does not appear to have any sort of seed argument. You could look at the inner workings of the function by typing `champ.norm` (no parentheses) into the console, which will you give you the function's code. I'd try and see which ...
written 3 months ago by jrleary130
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Comment: C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
... As quickly as I asked this, I figured it out. The hidden function `CalcN` performs this: ``` nCount = colSums(x = object, slot = "counts") # nCount_RNA nFeature = colSums(x = GetAssayData(object = object, slot = "counts") > 0) # nFeatureRNA ``` ...
written 3 months ago by jrleary130
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Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
... I'm converting a `SingleCellExperiment` object to a `Seurat` object, and I'd like to be able to regress out the effect of % mitochondrial DNA when running `SCTransform` for normalization & detection of highly variable genes. However, running `as.Seurat` does not add the necessary `nCount_RNA` or ...
scrna-seq R seurat written 3 months ago by jrleary130

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