Questions tagged [single-cell]

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

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2
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1answer
31 views

Using cellranger for non-10x data

I'm trying to use cellranger to mkfastq and then count and aggregate single-cell data. This ...
0
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1answer
44 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 ...
0
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1answer
42 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 ...
0
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1answer
47 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 ...
0
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1answer
67 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 ...
0
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0answers
27 views

How to find the differential gene expression between two samples

here are three samples' Dimplot. And I have a question about how to find the differential expression genes between Double-KO and Shox2-KO, for we can easily find the differential gene between the ...
0
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1answer
81 views

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

I would like to know how to change the UMAP use in the Dimplot and FeaturePlot by using Seurat, for we can get the x-axis and the y-axis like UMAP-1 and UMAP-2 if I want to use UMAP-4 and UMAP-5. How ...
1
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1answer
39 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 ...
0
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1answer
58 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 ...
1
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0answers
43 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 ...
0
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1answer
41 views

how to export the monocle data into Seurat

I have tried to export the monocle data into Seurat and got the error ...
0
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1answer
15 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 ...
0
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2answers
40 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 ...
0
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1answer
58 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 ...
0
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3answers
125 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 "...
1
vote
1answer
43 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
62 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
29 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 ...
0
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0answers
52 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. ...
0
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0answers
377 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
592 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
102 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 ...
1
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0answers
78 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
53 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
198 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
vote
1answer
41 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
33 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
135 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: ...
0
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2answers
355 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
votes
1answer
383 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, ...
0
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3answers
404 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
votes
1answer
531 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
192 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
46 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
votes
2answers
188 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
votes
1answer
158 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 ...
0
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1answer
68 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
673 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
votes
2answers
84 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
votes
1answer
179 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
333 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
vote
3answers
670 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
42 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
241 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
946 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
138 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
votes
1answer
44 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
302 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
405 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
votes
1answer
359 views

about dotplot legend meaning

Here is the code I used: ...