Questions tagged [seurat]

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18 views

Clustering information saved in Seurat object

Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to ...
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11 views

how to export the monocle data into Seurat

I have tried to export the monocle data into Seurat and got the error "Error in Seurat::CreateSeuratObject(raw.data = data, normalization.method = "LogNormalize", : unused arguments (raw.data = ...
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1answer
42 views

Putting cells in Seurat dimplot selectively

I am going to adjust Seurat dimplot in a way avoiding some cells so both my dimplot and heatmap look nice If you please consider this picture, you would see some cells are far from the clusters so I ...
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1answer
29 views

Seurat VlnPlot presenting expression of multiple genes in a single cluster

Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example: ...
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2answers
36 views

Trim Seurat object to contain expression info only for selected genes

I'm working with some large Seurat objects (MOCA, MCA, Tabula Muris) studying gene coexpression, and I'm running into memory issues. Is it possible to remove all genes in a Seurat object that are ...
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28 views

How to set equal distances between axes ticks irrespective of number of points I plot in a ggplot?

how can I set an equal distance between the ticks of axes in a ggplot irrespective of the number of items I plot? For example I want to have the kind of plot below from Seurat's ...
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1answer
39 views

different gene expression in the monocle

As it is shown in the picture that we can get the pseudotime plot by using Monocle. I was wondering whether we can use some function like the Seurat FindMarker to find out the differential expression ...
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1answer
53 views

How do I increase the minimum dot size in Seurat's DotPlot function?

I want to use the DotPlot function from Seurat v3 to visualise the expression of some genes across clusters. However when the expression of a gene is zero or very low, the dot size is so small that it ...
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3answers
83 views

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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53 views

Create a Heatmap that uses modules of genes rather than individual genes in Seurat

Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
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3answers
98 views

Understanding Single Cell RNAseq Plots

I have just started some single cell RNAseq analysis with 500 cells. I have used Seurat for analysis. Following the guideline I have generated few plots. Now I am trying to understand how to read ...
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188 views

Create heat map that groups genes by expression within cluster in Seurat

I have a set of cells that I am performing Drop-seq on to look at cell expression. Among my heat maps for gene expression I want to be able to graph them similar to the graph below: Where the cells ...
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38 views

how to cluster data separately based on HTO tags

If I have 2 samples hashed, ran together and generated one ADT file for them, then how do I plot 2 different ADT clusters separated based on the hashtags. I did use HTOdemux, but it shows me ...
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2answers
137 views

how to generate an scRNA counts file

I have barcodes.tsv, genes.tsv and matrix.mtx file from my RNA seq data and I want to generate a scRNA counts files using R. When I tried using the readMM function, ...
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1answer
122 views

Hierarchical clustering for outlier detection - single cell RNASeq & WGCNA

I wish to conduct WGCNA on a single cell RNASeq dataset and, when choosing the optimal beta parameter after running pickSoftThreshold am presented with a rather ...
3
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1answer
113 views

Subsetting of object existing of two samples

I have a Seurat object existing of an aggregate of two samples namely; RD1 and RD2. I am trying to make a subset of each sample. But it's not really working. I manage to make a subset of the cells but ...
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31 views

How can I figure out the cluster that low express in a specific gene in Seurat?

I'm following the standard protocol of Seurat so far and I know that Seurat can display the cluster that high express in a specific gene, however, I want to display the cluster that low express in a ...
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1answer
526 views

DoHeatmap Hierarchical Clustering Seurat

I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
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1answer
100 views

Cluster is split in 2-3 locations on tsne plot - Suerat

I am running a single cell dataset (count data - exon) through Seurat. After running tsne I see a cluster (13) split in 3 different locations on the plot. Here are the commands I am running: ...
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1answer
77 views

Why is 42 the seed used in RunPCA() in Seurat?

The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because ...
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2answers
253 views

How to create Seurat object while RNA expression and ADT combined into one matrix

I got an input matrix which RNA expression and ADT capture are combined into one file. I loaded the file into Seurat successfully, however, when I tried to create Seurat object, it threw out an error ...
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1answer
258 views

How to highlight specific cells in Seurat 2.4

I used Seurat 2.4 on our scRNA dataset to obtain the following tSNE plot.I was able to successfully extract cell IDs from the different clusters, and generate gene expression profiles. The analysis, ...
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3answers
278 views

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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79 views

convert ensemble ids to gene names within an object

How can I convert ensemble gene IDs (e.g. ENSG00000131142) to gene names (e.g. CCL25 ) within a Seurat object ? Thanks
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132 views

Subset cells based on a changefold level in gene expression

is there a way to subset a group of cells based on the foldchange of a gene expression? I have the KRAS object KRAS An object of class Seurat 53805 features across 6826 samples within 1 assay Active ...
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1answer
62 views

Enrich for genes expressed in the plasma membrane

I have a list of cell markers differentially expressed between 2 groups of cells, that I got with the FindMarkers command in Seurat. I want to enrich for those genes that are expressed in the cell ...
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1answer
81 views

Differential expression between two types of cells of specific marker gene expression

I want to define the identity of some cells based on a gene marker (for example the colour yellow< EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the ...
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1answer
191 views

How to set new identities for new clusters based on a gene expression in Seurat?

I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities. I clustered the cells and then created Violin ...
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1answer
160 views

Which values from Seurat::FetchData function are to be used for correlation analysis between genes?

I want to perform a correlation test between genes in on my single cell RNA seq data set. I perfomed the differential expression analysis using the Seurat version 2 package, after performing stages of ...
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78 views

Easy filtering seurat metadata based on knn results

Given a Seurat object I'm trying to get the metadata of neighbors cells (knn) to a given cell. I'm trying to create some score for each cell based on its snn neighbors. The score is: ...
2
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1answer
512 views

How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
3
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1answer
63 views

Storing FindAllMarkers results in Seurat object

I am currently working on multiple datasets where each is managed by a separate Seurat object. For each I'd like to also compute the marker genes using the ...
3
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1answer
231 views

Understanding PCHeatmap outputs

I am currently trying to understand the purpose of these PCHeatmaps - part of the seurat package in R: All the online documentation I have searched for has only ...
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2answers
176 views

Why are the clusters in the left side of a tSNE plot and not in the centre?

I have no idea why I used the subsetdata in Seurat after using CCA the TSNEPlot shows the cluster all in the left side and merge, did I miss something? Here are the code and figure I got. ...
2
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1answer
141 views

Why does my SplitDotPlotGG plot show differential expression of a gene but Seurat::FindMarkers() function does not return it?

I have analysed and clustered my single cell rna seq data with methods in the Seurat package. After clustering, I obtained two main clusters: 0 and 1. I used the Seurat SplitDotPlotGG function to ...
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1answer
507 views

how to obtain only one cluster's data (.csv file) in Seurat

I was using Seurat to analysis single-cell RNA Seq. And I was interested in only one cluster by using the Seurat. Does anyone know how to achieve the cluster's data(.csv file) by using Seurat or any ...
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0answers
34 views

failed to install hdf5r [duplicate]

I failed to install hdf5r using this command provided by https://satijalab.org/seurat/mca_loom.html: devtools::install_github(repo = 'hhoeflin/hdf5r'),below is the code,can you help me ?
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1answer
400 views

R studio failed to install the latest development version of hdf5r from Github (win10)

I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: When I use the second method to install from github,it showed many errors: ...
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2answers
527 views

How can I obtain the percentage gene expression per identity class in Seurat as further processible numbers (e.g. matrix)?

I am analysing my single cell RNA seq data with the Seurat package. I want to know if there is a possibilty to obtain the percentage expression of a list of genes per identity class, as actual numbers ...
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1answer
209 views

Percentage distribution of cells in all clusters based on their treatment condition?

I have 2151 cells, I clustered them by Seurat to 5 clusters. With the code below, I am able to have the number of cells per cluster and per condition: ...
3
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1answer
161 views

How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?

How can I prevent a function from sorting my data groups (factors) in alphabetical order without affecting the integrity of the data? I am analysing single cell RNA sequencing data using Seurat 2.3.4. ...
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1answer
529 views

How to set the position of groups in a Seurat object on a FeatureHeatmap plot

I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on ...
2
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1answer
376 views

Visualising gene expression across cell type and conditions in one plot, in Single Cell Sequencing data

I am new to single cell sequencing data analysis but I have basic programming background in R and python. I want to be able to plot differential expression of two genes, Gene1 and Gene2, across three ...
3
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2answers
797 views

Separate boxplots for multiple violin plot

I am using the following function from seurat package to generate multiple violon plots and I am interested in adding box plots to them but it doesn't work when I have plotted different data at once. ...
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2answers
825 views

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?
2
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1answer
165 views

ScaleData() from Seurat causes crash on RStudio Cloud

Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R ...
3
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2answers
343 views

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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1answer
132 views

Using external list of PCs for clustering

I am going to use principal components (PCs) comes from calcPCA function in URD program for clustering my cells in Seurat; So ...
3
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1answer
299 views

about dotplot legend meaning

Here is the code I used: ...
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1answer
219 views

Compare clusters from different datasets

I have two scRNAseq datasets, and I select a cluster from one of them, and another cluster from the other. I want to find differentially expressed genes between the ...