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Questions tagged [single-cell]

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

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2answers
34 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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1answer
14 views

Convert or extract Seurat object as the input of FateID

I am currently using Seurat to do the scRNA-seq clustering analysis. After this, I am planning to use FateID to do the downstream analysis, could someone teach me how to convert or extract a Seurat ...
0
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1answer
24 views

can we show the orig.ident in separate windows by using Seurat

I'm curious about can we show the orig.ident in sprat windows by using Seurat? Here are my code and the fig I got. Is it possible that I can separate each orig.ident into a single panel? ...
3
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1answer
25 views

public multi-modal single-cell data

There is a scRNAseq Bioconductor package with a few different example scRNA-seq datasets. Are there any R packages that offer multiple modalities of single-cell data? For example, hashtags or ADTs or ...
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0answers
44 views

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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0answers
73 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 ...
0
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3answers
118 views

how to merge more than two sample in Seurat?

I would like to merge more than two sample in the Seurat, and the mergeseurat can only merge two sample. So what should I do now. The screenshot is my script.
0
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1answer
40 views

Can I change the name of file features.tsv to genes.tsv

it is said that the features.tsv from Cell Ranger v3 is analogous to the genes.tsv from Cell Ranger v2. So can I change the file name to genes.tsv for Seurat to read it? I know that Seurat has the ...
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0answers
38 views

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 ...
2
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1answer
40 views

Single Cell RNA seq Analysis for low input Cells?

I am having a single cell RNA seq data from ~500 Cells. I do understand this number is very low for present day analysis tools like Seurat. So, I want to know what if one have a such a small number of ...
1
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2answers
83 views

making a customer reference by using cell ranger

Anyone here knows how to add a new gene (GFP) to customer reference by using cellranger? We use the Cre/loxp system by using R26RmTmG mice and want to use GFP to isolate specific cells. I have read ...
1
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1answer
27 views

semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
0
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0answers
28 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 ...
0
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1answer
57 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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2answers
177 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 ...
2
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1answer
127 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
174 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 ...
4
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1answer
348 views

PCA vs tSNE in single cell RNA-seq

What makes tSNE being the preferred dimensional reduction for visualization in single cell RNA-seq over PCA? I am aware that tSNE works better at showing local structures and fails to capture global ...
0
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1answer
120 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 ...
0
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1answer
43 views

how to write the script to know each sample's cluster number?

I have followed the Seurat Tutorial:Integrating stimulated vs. control PBMC datasets to learn cell-type specific responses by using my data. And I am confused about how to write the script to ...
2
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2answers
164 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
122 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
48 views

GEOquery errors due to list input

I want to extract the expression matrix from the GSE object in GEOquery. ...
0
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1answer
368 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 ...
2
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2answers
72 views

scRNA-seq differential transcript usage

Many of the modern gene-quantification tools (Salmon/Kallisto) output transcript-level (as opposed to gene-level) data. All of the scRNA-seq analysis I have seen just uses the gene-level values. I ...
0
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1answer
98 views

how to write italic script in Rstudio [closed]

I have got the problem on how to write the italic script in RStudio. I used the script in the screenshot and got the error "Error in grobs[[i]]: subscript out of bounds."
5
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1answer
225 views

How to normalise scRNASeq data for differential expression analysis

I wish to perform differential expression analysis for cluster-specific gene expression in single-cell data (with a tool such as MAST or SCDE). I have data for 3 biological replicates. I performed ...
1
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3answers
394 views

scRNA-seq,10x cellranger pipelines,low custom tdtomato gene content! looking for help!

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 ...
4
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0answers
40 views

Database of Cell Volumes by Cell Ontology?

Are there any databases that have aggregated information on cell volumes? Most useful would be a database keyed by cell ontology (e.g., CL:0000236 for B cell). ...
5
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1answer
131 views

Derive a GTF containing protein coding genes from a GTF file with Exons and CDS

Why I need a compatible file I’m trying to run velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x ...
3
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2answers
730 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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2answers
118 views

Can I get the graph generated by cellranger

I’ve run the cellranger analysis pipeline on single cell RNASeq datasets. I can import the matrix and graph-based clusters into R. Doing this I can optimise the dimension reduction and plot cells with ...
2
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1answer
41 views

What does that mean if there is no bifurcations in my time series single cell data?

Sorry, I have analysed my time series single cell data with Scuba algorithm but that says that there is no bifurcations in my data and outputted a single chain of 4 states with no branching like ...
3
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2answers
251 views

Collapse cell barcodes distribution within 1 Hamming distance

I have a barcode distribution from single-cell data, e.g: ...
3
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2answers
310 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 ...
3
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1answer
263 views

about dotplot legend meaning

Here is the code I used: ...
3
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0answers
38 views

What is the correct way of dealing with the analysis of data from flow cytometry?

I would like to detect a change in expression of a molecule present on a cell type by flow cytometry. Assuming I am able to detect, using an antibody, a signal that represents the amount of the ...
3
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1answer
50 views

Why is cell count stated relative to animal size?

Why do some single-cell RNA-seq papers give the number of cells sampled as a fraction of the size of the organ, animal, or embryo, as opposed to just saying how many cells they sampled? For instance,...
1
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1answer
65 views

How is PCR duplication rate computed in scATAC-seq?

Reading Cusanovich et al. (2015) I encountered the sentence: We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting ...
1
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1answer
1k views

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 ...
3
votes
2answers
2k views

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 ...
7
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1answer
69 views

Network comparison of single cells (from sequencing data)

What methods can we use to compare networks (PPI, gene regulatory etc) created from single-cell gene expression (or proteomics) data? There are methods that construct networks by comparing two ...
4
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3answers
3k views

Resolution parameter in Seurat's FindClusters function for larger cell numbers

In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
5
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1answer
114 views

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 ...
3
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2answers
971 views

What is cellranger doing in comparison to other methods?

I've recently started working with the 10X-Genomics platform with Illumina (MiSeq and HiSeq) for single-cell RNA-Seq. I've been recommended the "cellranger" (version 2.1.0) which I understand handles ...
4
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2answers
3k views

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 ...
3
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1answer
1k views

Subset on multiple genes in Seurat

I know that I can do subsetting on just one gene in Seurat: ...
5
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3answers
568 views

Regressing out unwanted sources of variation in single cell RNA-seq data

I have a dataset of single cell count data and I want to regress out the variation caused by the number of UMI's and the percentage of mitochondrial genes. I know that count data is discrete data, ...
11
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2answers
2k views

determining doublets in single-cell RNA-seq

Doublets are a known problem with scRNA-seq experiments, where 2 or more cells are sometimes captured instead. To determine their presence, there are studies that mix multiple species (such as human ...
5
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2answers
1k views

What are doublets in single cell RNA-seq data?

I am reading The Tabula Muris Consortium et al. (pp). In some organs, cells with more than 2 million reads were also excluded as a conservative measure to avoid doublets. How exactly is a “doublet”...