User: Pancreas Pratik

gravatar for Pancreas Pratik
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University of Connecticut
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Posts by Pancreas Pratik

<prev • 48 results • page 1 of 5 • next >
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Answer: A: How do I use FindAllMarkers after making additional cluster assignments?
... So this was solved with the help of @nbpeterson3 on the Seurat github Discussion page. So when FindSubClusters is done, it stores the subcluster in the object@metadata. Basically you have to use the SetIdent function to change the cluster assignments to your new cluster assignments. Here's a brief ...
written 5 hours ago by Pancreas Pratik110
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How do I use FindAllMarkers after making additional cluster assignments?
... Hey ya'll, This question is a follow-up question after the solution from here: https://www.biostars.org/p/492863/#492900 After subclustering using `FindSubCluster`, how do I `FindAllMarkers` using the additional cluster assignments on the whole `Seurat `Object? The cluster I subcluster is skipped ...
scrna-seq R seurat single cell-rna seq written 2 days ago by Pancreas Pratik110
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Answer: A: How to use FindSubCluster in Seurat?
... Okay so I got it... I think. I explored the Seurat object a litle bit more and found that the cluster assignments *were* saved. I was able to visualize using the `group.by` argument so here is the process: scfp <- FindNeighbors(scfp, graph.name = "test", dims = 1:100) scfp <- FindClus ...
written 2 days ago by Pancreas Pratik110
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Comment: C: How to use FindSubCluster in Seurat?
... Thank you @fracarb8. So I got the command to go through after this: I went to: https://satijalab.org/seurat/articles/multimodal_reference_mapping.html and Ctrl+F: `graph.name` Turns out graph.name is an argument in `FindNeighbors`. So I just use the FindNeighbors command choosing `graph.name` as ...
written 2 days ago by Pancreas Pratik110
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Answer: A: What Phenotype databases do you recommend for searching genes related to disease
... Okay. I think you'll like this alot. I downloaded this gene-disease pathway association database file from here: http://ctdbase.org/reports/CTD_genes_diseases.csv.gz Here is the link so you can explore: http://ctdbase.org/downloads/#gd I found 1918 unique genes related to Leprosy by doing the foll ...
written 2 days ago by Pancreas Pratik110
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Comment: C: Number of upregulated and downregulated genes from counts matrix
... Could you share a sample of your counts matrix? I'm not familiar with trinity (I'm not sure if there are built in functions within trinity to do what I'm suggesting below) If you just want to know which genes have positive expression values and which genes have negative expression values or if you ...
written 2 days ago by Pancreas Pratik110
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How to use FindSubCluster in Seurat?
... I just found the FindSubCluster tool within Seurat, and am super excited to use it. Just not sure exactly how! The usage is here: ``` FindSubCluster( object, cluster, graph.name, subcluster.name = "sub.cluster", resolution = 0.5, algorithm = 1 ) ``` I receive an error when using it. ...
R single cell rna-seq seurat written 2 days ago by Pancreas Pratik110
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How to interpret highly variable genes plot in Scanpy?
... Hey ya'll, How do I interpret this plot in the Scanpy Tutorial https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html: sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5) extracting highly variable genes finished (0:00:00) --> added ...
single-cell rna seq python written 5 days ago by Pancreas Pratik110
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Answer: A: How to deal with single nucleus data in Seurat
... Hi Kristina, Rpolicastro is right. There should be no difference in either using single *cell* RNA seq data or single *nuclear* RNA seq data with Seurat. A good place to start is definitely: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html Many of the steps are modifiable, based on you ...
written 5 days ago by Pancreas Pratik110
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Comment: C: How to record Seurat DE analysis efficiently?
... Oh, Okay. Thank you! I am thinking of playing around with trajectories at some point. Your approach definitely helped me gain additional exposure and understanding. Definitely going to refer back here. I don't think there are ready-made functions like this in Seurat. Thank you again! ...
written 5 days ago by Pancreas Pratik110

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Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Is there a way to use multiple processors (parallelize) to create a heatmap for
Scholar 11 weeks ago, created an answer that has been accepted. For A: Is there a way to use multiple processors (parallelize) to create a heatmap for
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