Questions tagged [scrnaseq]
Use this tag for questions related to single-cell RNA-seq.
276
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How to add ATAC data to a Seurat object using the Signac package without starting from an .h5 file?
I am attempting to run a multiomic analysis on some single cell RNA-sequencing data and ATAC-seq data. I have downloaded the scRNA-seq files from GEO in the format of (matrix.mtx.gz, features.tsv.gz, ...
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How to perform meaningful Gene set erichment analysis or otherwise find broader themes/functions in different cell populations?
(For context: I'm somewhat new to bioinformatic analyses but am mostly comfortable with R)
I have identified transcriptomically and morphologically different cancer cell populations within a patient (...
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Is it ok to shortcut cluster annotation in scRNA-seq?
I hope you all are doing well. I am currently conducting a scRNA-seq analysis on a data set containing mono-nuclear, non-myofiber muscle and muscle resident cells post injury. My research question is ...
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How to import data from cell ranger to R (Seurat) using Read10X?
I am loading cellranger data into seuratobject as following, but it keeps showing Error in
Barcode file missing. Expecting barcodes.tsv.gz
the running code and ...
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Done miRNA sequencing from animal tissue & have 1 control sample in duplicates 1 treatment group as test. In PCA plot clustering is not there
I have done miRNA sequencing from animal tissue and have control sample in duplicates . Like wise one treatment group as test. In PCA plot clustering is not there. There is very randomness. Is it ...
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Comparing sc-seq combination and bulk-sequencing
I have expression matrices for different cell types, representing the expression of individual cells of that type. They were learned through a generative model, so I am confident they represent the ...
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Looking for datasets of RNA-Seq (or scRNA-Seq) for L1 larvae C. elegans
I was wondering if anyone know of a repository for C. elegans data sets, specifically in L1 larvae stage.
Are there any papers or GEO-sets for this organism at this stage?
thanks
Assa
CommunityBot
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Why my FeatureScatter looks so different, and what does that mean?
I' am doing a sc-Seq analysis on a dataset from 10x genomics, using Seurat. I followed the standard workflow and I also did it with the SCTransform workflow. The results are very different when I plot ...
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Bar Graph of Expression Data from Seurat Object
I am looking for a way to present some single-cell RNA sequencing data on expression of a certain gene. My dataset has 2 variables, cell type and condition. I'm looking to create a grouped aligned ...
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What is a common number of cells per cell type in single cell RNA Seq?
Good afternoon,
I just started working with Single cell RNA Seq and I am trying to understand what is an average / possible number of cells per sample.
I am looking at a dataset of 7 patients with ...
CommunityBot
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Can anyone share insights or provide the complete mRNA sequence for tdtomato-WPRE for scRNA seq analysis?
I'm currently immersed in research involving the Rosa26-tdtomato (Ai9) mouse line. We performed scRNA seq and analysis focusing on tdtomato-expressing cells but faced a challenge with a lower-than-...
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Low custom tdtomato gene content
I have a set of scRNA-seq samples expressing TdTomato, which has high content in microscope. I followed the 10x cellranger pipelines to finsh the work, my procedures are as follows:
added TdTomato on ...
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Suggestion for way foward with upregulated genes
I am working with single cell RNA data- control and treated. I analyzed and got a list of upregulated genes. Upon doing pathway analysis all the genes were of apoptotic pathway. But these genes can ...
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Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads
I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit.
I have a question about using Knee Plot for identifying ...
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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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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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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 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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What column and row naming requirements exist with Seurat (context: when loading SPLiT-Seq data)
I'm trying to use Seurat for the first time and am learning about single-cell analysis for the first time, and I'm doing so with split-seq data. (Full disclosure: I'm also a lightweight when it comes ...
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Parsing gene names to detect organism from h5ad input
I have one function that is for reading .h5ad files
...
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Gviz Coverage Plots
This question has also been asked on Biostars
I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular ...
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Using CSV files continaing scRNA-seq count data from GEO [closed]
I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked a million times before.
I am trying to get the single cell expression data of lymph ...
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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 ...
CommunityBot
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is it possible to count cell in Violin plot in seurat?
I tried to quantify the number of cells of Fzd9+ Macrophage.
how can I know the cell count?
thank you
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How do cellranger and cellbender call cells? What is the difference between them?
When I use cellranger or cellbender to filter cell from raw RNA count matrix, the results they output are allways different. Each of then can call some cells not appearing in other's result. SO, how ...
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How to handle technical replicates in cellranger count?
I'm working with cellranger count to annotate some publicly available fastq files (SRX7888073). For each sample, 4 runs are available, which I assume represent technical replicates.
How do you ...
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h5ad file format filter
I'm trying to do simple filter for single data that is stored in h5ad file format using this
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Mapping single cell data with annotation
Entry level Bioinformatician here.
I am trying to map my single cell data with standard annotation file or assign my Seurat cluster to cell types. I have used the singleR and celldex package to map it ...
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Low fraction reads in cell metric in snRNA-seq data
For some of our snRNA-seq samples we are finding low fraction of reads detected in single-nuclei rna-seq samples from cellranger, while the other metrics are perfect.
While I understand this could be ...
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Correlate ssGSEA score with Seurat's scaled expression data
I want to check the correlation between the expression of a given "test_gene"* in each cluster within a scRNA-seq database with the expression of a signature (i.e., gene sets whose ...
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Merging multiple seurat datalist together
I have a R script that subsets out the tumor cells from 6 different individual seurat objects.
It gets a list of file paths for all RDS files containing the expression data for multiple datasets in a ...
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how to filter out cell after doing QC
I was wondering that the threshold that we set after doing QC in Seurat. there is an example
...
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Error in FindIntegrationAnchors- Seurat package
I am working on integrating a labelled single cell RNA seq cell atlas with an unlabelled one. I am wondering how do I determine the value of max.features when integrating two single cell RNA seq ...
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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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Gene names from components in NMF analysis
This question was also asked on Biostars
I am using Rcppml package in R for my NMF analysis, I have a matrix from single-cell analysis. I have cells scores and I wanted to know how to extract genes ...
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How to remove orig ident. already data normalized, scaled assigned cluster/
How to remove orig ident. already data normalized, scaled assigned cluster/ Example, I have 4 sample data. like 1-control, 2- treatment with A, 3- treatment with B, and 4- treatment with C,
I want to ...
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Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
I can't seem to find a clear answer to this question, so here it goes:
I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
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In cellranger, can I change the minimum number of reads for autodetecting chemistry?
I ran cellranger multi on a TotalSeq B dataset and got this error
...
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How to calculate cell type percentage in every sample
I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I am trying to make a table that has a sample and percentage of cell types for each ...
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Determine expression values for a defined list of genes across different clusters in scRNA data using seurat
I am analyzing publically available scRNA seq datasets on R using Seurat. I have created a seurat object, clustered and annotated different cell types. Now, I am interested in comparing the expression ...
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How to plot average gene expression in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.
I did ...
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How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.
I did ...
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Cells with zero expression of a given gene
I have scRNA-seq from PBMC analyzed by Seurat. I am seeing for most of genes a lot of cells have a zero expression like this gene
So 268 single cells have the expression level == 0
And I am more ...
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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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Can 5' end 10x be used instead of 3' end
I have PBMCs of some patients who have recovered from cancer, and I want to look at their immune landscapes.
I got confused when looking at available kits: can I use 5' end kits from 10x instead of 3' ...
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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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Creating meta cells from scRNA-seq and scATAC-seq for GRN analysis
We have two 10X Genomics scRNA-seq and scATAC-seq datasets generated from similar cells, but in different experiments - separately, not using the multiome platform. Now, we are trying to use Pando (...
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How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?
The cell subpopulation that I am interested in only accounts for around 1.2% of the total cells. I have previous FACS experiments that sort out the subpopulation from the samples (using markers CD166+ ...
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pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
...
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