Questions tagged [seurat]
Seurat is a package for analyzing single cell rna seq data.
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Different colors in UMAP
I have integrated top ten TCR clones into Seurat object something like below
You are seeing some clones are expressed in more than one cells
So in Seurat I have something like
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Merging two seurat objects
I want to merge 2 Seurat objects together, the first object is purely aligned to human but the second object comes from PTX samples so aligned to both human and mouse. In order to just get the human ...
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Violin plots appear as vertical lines
I want to perform a violin plot from a Seurat object and I rather have vertical lines. How can I stop this and rather have a standard Violin plot?
code
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Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?
As we know, the amount of RNA reads per cell obtained from 10X scRNA experiment vary between cells. I wonder if this is effect of technical issues or does the number of RNA reads per cell obtained ...
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How to manage memory contraints when analyzing a large number of gene count matrices? I keep running out of RAM with my current pipeline
I have several hundred scRNA-seq count matrices, each from a different sample. For my other dataset containg a few dozen samples, I simply merged everything together into one Seurat object, but that ...
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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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Subsetting out prefix from genes and merging
I'm working with PTX samples (human and mouse), they're aligned to both transcriptomes and so gene names contain hg38- and mm10- at the beginning of each gene. I have eliminated teh prefixes because I ...
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DimPlot - How to highlight cells with identity colors?
I made this wrapper for DimPlot:
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How will Seurat handle pre-normalized and pre-scaled data?
I want to use data from the following dataset:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84371
The data has been TPM normalized, which is not ideal for clustering but I have to work with ...
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Seurat Integration
I'm following the instructions for integration:
https://satijalab.org/seurat/articles/integration_introduction.html
And it's taking a while to run:
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Pulling normalized gene expression data across cells from Seurat object
I want to pull gene expression out of a seurat object. I created one called combinedObject following their tutorial, I normalized scaled it etc and created some ...
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Plotting a gene in Seurat
I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice.
<...
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Featureplot by co-expression of some genes
I want to identify MDSCs cells which don't not express HLA-DRs (HLA-DR negative) but express ...
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(scRNA-seq) I have a dataset with 4 conditions (experiments) should I be anchoring aka integrating data for each comparison when looking for DEGs?
I have an experiment with 4 conditions in it two of them are controls. When I am correcting for batch effects (either with PCA or CCA) should I restrict my comparisons between particular groups? So ...
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Integrating scRNA-seq data using raw data
I am trying to reporduce the the following article Chen, M. B., Jiang, X., Quake, S. R., & Südhof, T. C. (2020). Persistent transcriptional programmes are associated with remote memory. Nature, ...
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Assigning subcluster idents to original object
I have a scRNA-seq Seurat object I've analyzed, and I noticed that for some of the clusters, there's more than one cell type.
I've created a subset which and run FindClusters again to label the cell ...
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How to split a Seurat cluster in several subclusters?
I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. (for example, cluster 9 shows both NK and CD4 cells)
How can I split a cluster ...
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Using different "principal components" in UMAP visualizations
In certain UMAP visualization, it appears that the visualizations show the first UMAP "principal component" plotted against the second. For example, like this:
Apparently, this lets us use ...
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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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Error in colSums(cts[[i]]) : 'x' must be an array of at least two dimensions
I'm getting an error when creating the counts from a single cell experiment.I'm identifying shared barcodes as well as lowUMI barcodes with the follow code:
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FindMarkers from Seurat returns p values as 0 for highly significant genes
I have been working on FindMarkers function for identifying significant genes in the cluster. But some Significant genes have very low p values, so they are returned as 0 in the output.Any value less ...
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CITEseq different sequencing depth normalization -- Seurat
New technician ruined his first 10X CITEseq experiment on cells counting level and the ratio between replicates is 14k:2.2k:0.8k ncells.
How should I now normalize protein data (ADT) from experiment ...
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In Seurat, how can I export cluster IDs to csv files
I am doing scRNAseq analysis with Seurat.
I clustered the cells using the FindClusters() function.
What I want to do is to export information about which cells belong to which clusters to a CSV file.
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Calculating percent mouse cells per sample
I want to see the correlation between % mouse reads per sample vs % mouse cells per sample. I've already calculated the % mouse reads per sample but I'm stuck on calculating the % of mouse cells per ...
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Removing columns from meta.data in Seurat
I'm trying to remove columns from the meta.data from a Seurat object. Is there a way to do that or would I have to re-create the Seurat object without that column?
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231
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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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How to calculate species fractions in Seurat
I'm working with a PTX dataset and I'm trying to calculate species fractions based on read count instead of cell count.
Would just be a matter of taking the raw counts matrix of cells x gene per ...
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317
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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 ...
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Problem with Seurat reference mapping
I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC
Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for ...
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Understanding the dot plot from seurat
I am working with single cell data and using seurat to analyze the results. Often in manuscript, we see the dotplots showing the expression of the marker genes or genes of interest across the ...
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Seurat - single cell analysis
I have been doing single cell analysis based on seurat and I realized after each clustering and reclustering when I run SCTransform, in my code there is vars.to.regress = percent.mt and I was running ...
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sctransform - mitochondrial expression filtering / transformation
I have a Seurat object which has a high expression of mitochondrial genes
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116
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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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Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat
I have a Seurat object
I want to plot a list of genes but I got a warning saying most of genes removed
I have tried with both my genes of interest and all variable genes but the results is very ...
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1
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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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75
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TCR-seq or scRNA-seq
I need idea, intuition, suggestion please
I have 10X scRNA-seq of PBMC (multiome's 3' poly-A capture), can I capture ...
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Making a box plot of the proportion of cells in each cell types in two groups
I have number of cells in three cell types T, B, M in a Seurat object
For two groups of patients, cancers and controls like
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2
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SCTransform Warning: in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Running SCTransform on my seurat object produces the warning:
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
What does this warning mean? ...
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63
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Merging two dataframes in R
I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like
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154
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Filtering cells from values in metadata
I metadata slot of Seurat object I have mapping score of each cell to a reference PBMC data like
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What does this Seurat argument mean
I have extensively read about percent mito in Seurat but I got more and more confused
Let's say we want to keep cells with ...
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263
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Seurat Dimplot with different clustering IDs
In Seurat metadata I have assigned cells to some cell types with different resolutions
I have added the cluster identities to the object via Idents:
...
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color by clusters and sampled in Seurat
I have a Seurat object
I want to have both cluster numbers and coloured cells by sample names like this figure (from a Nature paper)
I have tried group.by argument ...
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Adding metadata to Seurat object
I have a Seurat object of 8 patients. I want to add metadata to that so that I have origin of each cell. At the moment UMAP just shows a bunch of cells while I want to color clusters by sample
This is ...
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Seurat clustering Methods-resolution parameter explanation
I am learning the Seurat algorithms to cluster the scRNA-seq datasets. I found this explanation, but am confused. Can someone explain it to me, "The FindClusters function implements the procedure,...
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261
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"variable.features.n" in SCTransform
Whats the role of "variable.features.n" in SCTransform function of Seurat? I try setting "variable.features.n" at three different numbers (2000, 5000, 10000). In the downstream ...
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