Questions tagged [single-cell]

Questions about techniques in which the genetic material of a single cell is analysed individually

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31 views

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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3answers
53 views

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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2answers
47 views

How to find differential expressed genes within pseudotime trajectory with Seurat cluster?

Did anyone know how to find the differential expressed genes within pseudotime trajectory with Seurat cluster? In monocle tutorial, we can use BEAM to find the differential expressed genes between the ...
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2answers
63 views

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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11 views

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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1answer
27 views

What is meant by transcriptional changes executed by the cell over a time period?

I read the following line in the research paper - The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells: During differentiation, for example, each ...
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20 views

A very large number of clones in BCR reportorie

I am using mixcr to convert fq.gz raw data file (single cell BCR sequencing) to txt files with the names such as JX01_d3-B.clonotypes.IGH.txt , Then I use the immunarch to load the file to explore the ...
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1answer
89 views

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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48 views

functions in seurat to calculate the gene count per cluster

I'm running FindAllMarkers ...
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81 views

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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1answer
306 views

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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2answers
98 views

10X scRNAseq: Sample mix-up

The student who was working on scRNA seq of KO and WT lines has made a mistake and he mixed both lines and generate the final sequencing data. Now, we are having gene expression data but don't know ...
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1answer
45 views

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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46 views

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 ...
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1answer
49 views

Seurat - subsetting by genes expressed

Originally- I was looking if in at least one of these genes were expressed: ...
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18 views

Average ratio of spliced and unspliced mRNA in human scRNA-seq data

I am currently doing RNA Velocity Analysis using scRNA-seq data from human blood and skin. The RNA Velocity is calculated using the balance of spliced and unspliced mRNA. One thing my PI and me were ...
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1answer
151 views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
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1answer
51 views

Challenging benchmarks for supervised learning on sparse scRNA-seq data

One challenging aspect of modeling scRNA-seq data is data sparsity, that is, scRNA-seq measurements typically suffer from large fractions of observed zeros (i.e. dropouts), where a given gene in a ...
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1answer
41 views

Segment cell organelles with pixellib

I've got some images of cell organelles and I really want to avoid labeling them by hand. The images all look something like the image below. Is there already an existing model specifially for cells? ...
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1answer
149 views

How do I change the identity of a sample from spatial 'Visium' data preprocessing in Seurat v3?

I'm wanting to create a merged object in Seurat using 2 10x Visium 'slices'. However, when I create an object, Seurat assigns an identity "SeuratProject" to the objects (by default I'm ...
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3answers
69 views

Where can I find Single Cell Data with Location "Coordinates"?

Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? ...
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1answer
162 views

Calculating average mito.percentage for each cluster (seurat)

I have a tricky data set with cells that will have a higher percent of mitochondria genes than "typical" data sets. I would like to look at the mito percentage in each cluster without any ...
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2answers
162 views

Single cell RNAseq cell cluster (true cluster or sub cluster)

I am trying to run seurat on ~5000 sinngle cells. I am expecting minimum 15 cell types to be present in the data. I tried to runn it with multiple conditions;I can see there is 27 clusters; I believe ...
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37 views

which marker identifications method is recommended when single-nuclei RNA seq datasets are integrated across regions

I'm analyzing Sn-RNA seq datasets which include different brain regions and spinal cord in patients and normal controls. I would have different comparison within and between individuals. I've got a ...
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1answer
97 views

What is the best way to address the question of doublets and multiplets in a single cell RNA seq data set?

I have attached a histogram plot of the number of genes per cell in a single cell RNA seq data set of lung endothelial cells. I do not find a bimodal or multimodal distribution of the number of genes ...
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1answer
263 views

Help with setting DimPlot UMAP output into a 2x3 grid in Seurat

On my merged seurat object of 6 samples, when I use the split.by function in tandem with the Dimplot/UMAP plot, all six samples are displayed in series along a commonly labeled 'UMAP_1' x-axis in an ...
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2answers
69 views

How can I take cell number into account to find total RNA expression?

I'm hoping to quantitatively show differences in total RNA expression for a gene in a cluster of interest between different experimental groups. My exported average RNA values for each experimental ...
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1answer
474 views

Adding treatment groups via metadata to Seurat object?

I'd like to add metadata to 6 individual Seurat objects so that after I merge the objects into one, I can later label or split by using these identifiers. For example, I'd like to append an age group ...
2
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0answers
90 views

scRNA-Seq: Account for sequencing depth and gene length?

Task: Normalize a single-cell RNA-Seq dataset to account for sequencing depth and gene-length. For UMI-count based protocols (like 10x) that don't suffer from gene-length biases, there are various ...
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1answer
29 views

GSEA enrichr with 10x genomics differential_expression ranks

I am attempting to use GSEA enrichr with 10x genomics differential_expression rankings. Reading what people seem to be doing with GSEA, there seems to be a pre-/post-singlecell gene expression ...
2
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3answers
370 views

How to reduce the occupied RAM when you are dealing with a very sparse matrix in a single-cell Experiment in R?

I'm dealing with a very large and sparse dataset and the first issues I met occurred when I tried to use quickCluster that reported me this error: ...
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70 views

Seurat analysis only with matrix with no barcode and features

I have downloaded a dataset from GEO and only the matrix (mx) files are available. How can I perform the analysis without the barcode and the gene features?
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3answers
451 views

umap and Louvain clustering on normalized data

I know that scaled data must be used for PCA for example as it is based on variance maximization. However I'm wondering if it's the same case for UMAP ? If the data are single-cell RNA seq, after ...
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1answer
36 views

Is there a single cell RNAseq equivalent of GTEx or TCGA? [closed]

Or do I need to find individual studies and obtain data the long way!
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2answers
1k views

Adding certain barcodes to metadata in Seurat

I want to upload an excel file sheet that has certain barcodes that I would like to show on my umap. How do I go about adding the file and linking it to the metadata? Below is my following code. <...
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2answers
1k views

Is there a command line tool to split a SAM/BAM file by CB (cell barcode) tag?

I have a BAM file from a single cell sequencing experiment. Each read has had the cell barcode annotated in the CB tag. Some reads do not have a ...
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0answers
404 views

Understanding BuildClusterTree of Seurat

I am trying to understand how to use BuildClusterTree of Seurat to understand the relationship between clusters. Being from neither a bioinformatics or statistical ...
2
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1answer
93 views

Using cellranger for non-10x data

I'm trying to use cellranger to mkfastq and then count and aggregate single-cell data. This ...
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1answer
215 views

Stacked barplot for single cell analysis

I want to create a stacked bar-graph with different cell cycles for each cell type within each condition. I have uploaded the file for it. Don't know how to go about it as now I have another condition ...
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1answer
153 views

Single-cell sequencing dataset has too many barcodes

I am analyzing a single-cell sequencing dataset from the website 10xgenomics, with 2000 cells. It is a BAM file and I am trying to obtain the individual cells per sample. I used the command ...
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0answers
518 views

Low Fraction of usable antibody reads in CiteSeq

we performed a combined gene expression and CiteSeq experiment with the 10x VDJ kit and 20 conjugated antibodies and sequenced on hiseq. I used cellranger to process the sequencing output. The ...
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1answer
185 views

Finding differentially expressed genes between two samples

Hi, I was wondering whether we can find the differentially expressed genes between the Double-KO and the Shox2-KO. For the ...
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2answers
1k views

how to change the UMAP use in the dimplot and feature plot

I would like to know how to change the UMAP used in Dimplot and FeaturePlot from Seurat: how we can get the x-axis and the y-...
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1answer
305 views

how to change the PC use in the dimplot and feature plot

I would like to know how to change the PC use in the dimplot and featureplot by using Seurat. for we can get the x-axis and the y-axis like PC-1 and PC-2, if I want to use PC-4 and PC-5. How to modify ...
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1answer
291 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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0answers
45 views

Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
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1answer
257 views

how to export the monocle data into Seurat

I have tried to export the monocle data into Seurat and got the error ...
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1answer
33 views

Calculating celltype proportion changes between conditions in single-cell data

I want to test for significance between differences in cell count between conditions. I have 2 conditions (N, T), 3 donors (samples) each, and four cell types (A-D) as shown in the example below. I ...
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2answers
116 views

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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1answer
168 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 ...