User: Apoorva

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Apoorva270
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Posts by Apoorva

<prev • 72 results • page 1 of 8 • next >
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Answer: A: Error :[[<- defined for objects of type "S4" only for subclasses of environment
... I'd updated seurat from 3.0.2 to the cran version (3.2.2) when I started having this issue. Uninstalling and reinstalling Seurat with all the dependencies didn't work either. Weirdly enough, updating uwot and installing the v4.0 beta fixed it. ...
written 1 day ago by Apoorva270
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Answer: A: Shiny board with seurat object
... You have to use the DimPlot function in place of plot(input$dataset, reduction = "umap") Try DimPlot(input$dataset, reduction = "umap") ...
written 1 day ago by Apoorva270
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Comment: C: Error :[[<- defined for objects of type "S4" only for subclasses of environment
... Yes it is. Because there are no issues displaying a FeaturePlot or a table of differentially expressed genes from the dataset. ...
written 1 day ago by Apoorva270
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Error :[[<- defined for objects of type "S4" only for subclasses of environment - Shiny App error
... I have an application built in shiny that uses the [Seurat](https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html) package. I'm using one of their plotting functions (DimPlot) to view the tSNE and UMAP plots within the application. This app works perfectly fine on my local machine. But when i host ...
single cell rnaseq shiny seurat written 1 day ago by Apoorva270
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Comment: C: Aligning multiple runs using STARSolo
... Thank you very much. I was looking at the STARSolo documentation and it mentions so for multiple lanes. ...
written 10 weeks ago by Apoorva270
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Aligning multiple runs using STARSolo
... Hi all, This question might be basic but it has gotten me confused. I download single cell RNASeq data for a sample from GEO using SRAtoolkit. As you can see [here][1], this particular sample has 4 runs. So when running [STARSolo][2] using the following command, would it be right to comma-separate ...
single cell rnaseq alignment scrna star starsolo written 10 weeks ago by Apoorva270 • updated 10 weeks ago by ATpoint44k
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Answer: A: sratoolkit prefetch command returns no result
... Turns out the server doesn't have an outbound network access. My bad. Sorry. Will have to do it locally. ...
written 10 weeks ago by Apoorva270
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Comment: C: sratoolkit prefetch command returns no result
... That is just an example. I have the issue for any SRA file i try to download using prefetch. It works fine when I run it on my local directory. But what I really want to do is to use it to download the files to a remote server that has sratoolkit installed. fast-dump works on it. Just not prefetch. ...
written 10 weeks ago by Apoorva270
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sratoolkit prefetch command returns no result
... Hi everyone, I recently updated my sratoolkit from version 2.8 to 2.10.8. Now my prefetch command doesn't seem to be working. I tried this `prefetch -p SRR8387813 -o ~/SRAfiles/sra`. It runs for some 5-10 mins. No progress messages despite the -p argument. No error messages. But then the file does ...
sratoolkit written 10 weeks ago by Apoorva270 • updated 10 weeks ago by ATpoint44k
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Downloading single cell RNASeq data using SRA
... Hi, I'm trying to download a single cell RNASeq dataset from GEO to run my analysis on them. I need the 3 fastq files to begin with (R1, R2 and I1). prefetch SRR9313701 I used sra toolkit and got the .sra file using the prefetch command and then I ran fastq-dump to split them. fastq-dum ...
single cell rnaseq sra toolkit written 4 months ago by Apoorva270 • updated 4 months ago by ATpoint44k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Removing batch effects from RPKM data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
Great Question 2.3 years ago, created a question with more than 5,000 views. For PCA plot of RPKM data from RNA-Seq dataset
Popular Question 2.3 years ago, created a question with more than 1,000 views. For MACS2 Peak Calling : Different number of peaks for each replicate
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