All Questions
Tagged with single-cell r
25 questions
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Demultiplex double hashed cells using Seurat (R)
I am using Seurat to demultiplex my single-cell RNA data, which also has HTO data for hashing. Each cell is hashed once based off it's origin ie organ1, and then hashed based off the cell type ie cell ...
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Plotting infercnv results
I'm working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package.
I've ...
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2
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422
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Error in dimnamesGets(x, value) when trying to read data using Seurat package
This question has also been asked on Biostars
I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
- 21
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353
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Subsetting with harmony
Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA?
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2
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814
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Reading in external single cell data
I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix.
counts found here: https://www.ncbi....
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2k
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ViolinPlot x-axis
I'm trying to set the x-axis in my Violin Plot to go by each patient rather than it being scattered.
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- 391
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2
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2k
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Subsetting a Seurat object based on colnames
I'm trying to subset my seurat object based on colnames. I have gone ahead and labeled each cluster and now I want to subset all the colnames that are in Cancer_human for human_colnames and all the ...
- 391
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296
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217
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Creating new seurat object with new matrix
I'm trying to do a cross-species comparison between the patient TME vs. the PTX TME to understand gene expression conservation. I have already converted between mouse and human genes giving me a ...
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converting mouse genes to human genes
I'm trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I'm using this file for the orthologs.
http://www....
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-1
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2
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Unifying these files together [closed]
I have two .csv files
One for raw read counts of each gene and the other 3114 single cells for four patients which should be the row names of the first file
As single cells per patients seems ...
- 2,232
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2
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248
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Uploading files from local computer or web in rstudio cloud
I am using RStudio Cloud for running velocyto R package. So I have tried to import velocyto file from http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom
I tried to upload that like so
But ...
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3
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3k
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Which correlation method to compute the correlation score between different clusters of Sc-RNAseq data?
I'm analyzing single cell rna-seq data and trying to compute the correlation score between different clusters. Wondering how to choose the correlation method("pearson" (default), "kendall", or "...
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1
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1
answer
271
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length of 'dimnames' [1686] must match that of 'dims' [3]
Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion.
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- 547
1
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152
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Error using bseqsc
I will be very grateful for any hint on how to overcome the error. I wish to deconvolve my bulk RNA seq data obtained from the lungs of mice using single cell RNA seq data. For practice, I am ...
- 547
2
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3
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3k
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Import gene list to Seurat to define cell types
Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but ...
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2k
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Using Seurat to compare mutant vs.wt
I am interested in using Seurat to compare wild type vs Mutant. I don't know how to use the package. How can I test whether mutant mice, that have deleted gene, cluster together?
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1k
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Changing a wide range of colours to a limited gradient
I returned a FeaturePlot from Seurat to ggplot. My plot has a weird range of colours as below
I produced this plot by this code
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3
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1
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2k
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1
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1
answer
2k
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Violinplot of gene expression
I have plotted the log normalized expression of two genes by violonplot for 4 clusters. I have links to my pictures and Seurat object too. My problem is this; in violin plot I can not see the mean or ...
- 2,232
3
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3
answers
6k
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Mapping a list of cells in seurat featureplot
I have 209 cells, I clustered them by Seurat to 4 clusters. By Featureplot I am able to track a gene in clusters:
Higher color shows higher expression.
Now, for some genes I want to highlight some ...
- 2,232
7
votes
3
answers
16k
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Finding the optimal resolution parameter in Seurat's FindClusters function
In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
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5
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1
answer
220
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Which are the use cases for the methods for DE in Seurat
In Seurat we can specify multiple methods for finding DE genes.
I am wondering when should we use which one, the use cases. As ...
- 2,578
5
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2
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14k
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Manually define clusters in Seurat and determine marker genes
I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...
- 2,578
4
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1
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3k
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Subset on multiple genes in Seurat
I know that I can do subsetting on just one gene in Seurat:
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