Questions tagged [single-cell]

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

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Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?

I have single cell data which I want to annotate with the seurat package, so I ran this code in R: ...
Rita Soares's user avatar
1 vote
0 answers
10 views

Identification of metabolites through spectral library search

I am very new to single-cell metabolomics and today I want to jump in this area. I have been reading many review papers related to identification of metabolites at single-cell resolution from spectral ...
Huy Nguyễn's user avatar
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1 answer
87 views

scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?

I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...
Henry Gong's user avatar
1 vote
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Parsing gene names to detect organism from h5ad input

I have one function that is for reading .h5ad files ...
kcm's user avatar
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-1 votes
1 answer
142 views

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 ...
Newbie Bioinformatician's user avatar
1 vote
0 answers
282 views

Loading scATAC-seq data containing matrix.mtx, fragments.tsv and barcodes.tsv files from GEO into R?

I want to analyse the single-cell ATAC-seq data from 10X downloaded from GSE158398. The files attached to this dataset are matrix.mtx.gz, ...
Embla's user avatar
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3 votes
1 answer
55 views

What trajectory analysis method allows to set the form of the trajectory?

I have single cell data from two samples : normal and pathological and I would like to track the progression of the cells (and find the genes that drive it) from normal to pathological. Upon first ...
Sam's user avatar
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2 votes
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108 views

Cell Ranger returns too few cells!

I recently performed single cell RNA seq using core services and the web summary output from 10x that they have given shows that there are very few cells detected (100-300) cells per sample. Once this ...
Abhishek Dubey's user avatar
2 votes
0 answers
49 views

shiny app for single cell cluster export issue

I'm trying to create a shiny app for single cell data visualization and then label cells with genes till this step it works, the final step when I try to export cluster it is not exporting the desired ...
PesKchan's user avatar
  • 207
1 vote
2 answers
752 views

Plotting infercnv results

I'm working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package. I've ...
mmpp's user avatar
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1 vote
2 answers
237 views

h5ad file format filter

I'm trying to do simple filter for single data that is stored in h5ad file format using this ...
PesKchan's user avatar
  • 207
2 votes
0 answers
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Find Lipidic Mediator receptors

I want to study the ligand-receptor interaction and I am searching for lipidic ligands( mediators), I have found 16 so far. Does anyone know any database where I could find more lipidic ligands. I was ...
Mariam Ismail's user avatar
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121 views

How to check average gene expression for each of 2 conditions within a cluster in scanpy?

I used scanpy to do DE analysis for 2 conditions within a cluster. I set it up like shown here: ...
pythonbeginner's user avatar
4 votes
1 answer
60 views

Identifying somatic mutations in cell lines

I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a ...
Macintosh's user avatar
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1 vote
2 answers
552 views

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 ...
Yogesh Budhathoki's user avatar
2 votes
0 answers
175 views

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 ...
pythonbeginner's user avatar
2 votes
0 answers
71 views

Can I use palantir for trajectory analysis in a a merged object?

I was asked to use palantir for trajectory analysis. I have 4 samples that I have preprocessed using scanpy. Can I run the palantir analysis on the merged object or do I need to unmerge them? Thank ...
pythonbeginner's user avatar
-1 votes
2 answers
468 views

How to do pathway analysis after scanpy for single cell data after DE analysis?

I have done DE analysis using SCANpy on my single cell data and I have compared each cluster versus all the other clusters. One cluster seems particularly interesting so I wanted to do pathway ...
pythonbeginner's user avatar
2 votes
1 answer
54 views

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+ ...
Wang Ming's user avatar
  • 101
2 votes
0 answers
120 views

pyScenic CLI for ctx is giving error: Not a single module loaded

Hi I ran pyScenic's ctx via the command in command prompt: ...
Yihua's user avatar
  • 21
1 vote
1 answer
174 views

How many percents explained variance by the first 50 principal components of PCA analysis is suitable for downstream `KNN` and `umap`?

In single-cell RNA sequencing analysis, I am wondering how many percents explained variance by the first 50 principal components of PCA analysis is suitable for downstream ...
Dan Li's user avatar
  • 141
3 votes
0 answers
201 views

How to concatenate 2 `mdata` of `muon` package?

I used muon(https://github.com/scverse/muon) for single cell Multimodal omics analysis. How to concatenate 2 mdata from ...
Dan Li's user avatar
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2 votes
0 answers
100 views

Is there a package that can filter the `raw_feature_bc_matrix` of 10X's `cellranger multi` pipeline output?

There is no filtered_feature_bc_matrix in 10X Genomics' cellranger multi pipeline output when multiplexing analysis was ...
Dan Li's user avatar
  • 141
1 vote
1 answer
712 views

Best method to compare differentially expressed genes between 2 single cell clusters for GSEA

I want to get a ranked gene list for GSEA analysis from single cell data, which needs a group differential expression statistic for ranking. Which is the best method to compare the differently ...
Dan Li's user avatar
  • 141
1 vote
1 answer
113 views

How to preserve colour assignments in matplotlib when a category is empty?

Some of my samples have empty clusters. I want to keep the same color for each cluster in different plots. How do I get sc.pl.umap to keep the same colors for each ...
Dan Li's user avatar
  • 141
1 vote
1 answer
138 views

umap failed to cluster the cells

I tried umap visualization with scanpy : ...
Dan Li's user avatar
  • 141
1 vote
1 answer
112 views

FlowSOM multi-step clustering

There are a few different commonly used clustering algorithms within the single-cell space, although Leiden seems to be the top choice these days. FlowSOM is a classic package for analyzing flow ...
burger's user avatar
  • 2,179
3 votes
2 answers
1k views

How to extend the x axis in Dimplot Seurat

I have performed a Seurat PCA via Dimplot. How do I extend the x axis? As you can see in my figure the double x axes overlap.
cow's user avatar
  • 43
1 vote
1 answer
20 views

Definition of genotype in demuxlet

I am reading the Online methods of the demuxlet paper. The genotype $g$ is taken from the set $\{0, 1, 2\}$, defined as "the true genotype of the sample corresponding to $c$-th droplet at $v$-th ...
gc5's user avatar
  • 1,783
1 vote
2 answers
304 views

Error in dimnamesGets(x, value) when trying to read data using Seurat package

This question has also been asked on Biostars I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
Gen's user avatar
  • 21
0 votes
0 answers
423 views

extracting raw gene counts based on the cluster generated by seurat

I'm new to single cell sequencing analysis. I have made different clusters using seurat. Now I would like to extract the raw gene counts based on the cluster generated by seurat. i have provided my R ...
Manojkumar K's user avatar
1 vote
0 answers
126 views

Identifying highly variable genes in scRNA-seq: Seurat vs M3Drop

Following a single-cell RNA-seq workshop, I created a Seurat object (my_data), normalized the data, and then tried to identify highly variable genes using two ...
Judit's user avatar
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2 votes
0 answers
88 views

snRNA-seq Demultiplexing before or after QC

I'm currently analyzing snRNA-seq data and have to demultiplex them using HTODemux in Seurat. The question is : should I do my QC filters on my droplets before or after the demultiplexing ? From what ...
AlixSil's user avatar
  • 21
1 vote
0 answers
32 views

how to change the pseudo time trajectory direction?

Monocle is a comprehensive bioinformatics package which has the function to run the pseudo-time trajectory and changes in direction. I wish to replicate this analysis. Like in the figure I would like ...
cow's user avatar
  • 43
1 vote
1 answer
42 views

How can to validate the presence of a certain type of cells in a single cell dataset?

I have a single cell dataset which I consider to be a reference , let say, for an human organ, I have identified some new clusters that correspond to cell types. I also have WGCNA modules that ...
MrPapouille's user avatar
1 vote
1 answer
778 views

Cellranger results have too many cells

I have the results of cellranger analysis for single-nucleus RNA seq data that was done by someone else. So I do not know which parameters were used for cellranger. In the results, there are 77000 ...
Yulia Kentieva's user avatar
1 vote
2 answers
2k views

How to convert 10x matrix.mtx.gz files to hdf5 format?

I have a bunch of folders containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz from the Cellranger Count output for a single-cell dataset that was sent to me from another lab. I need the .h5 ...
Johnny Rocketfingers's user avatar
1 vote
1 answer
101 views

How can I get data of single cell RNA sequence with raw count?

I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values. How can I find the read counts of a dataset?
Kevis Lin's user avatar
4 votes
2 answers
136 views

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 ...
Karol Jacek's user avatar
1 vote
0 answers
32 views

What genes are driving a certain pathway

I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway. ...
mmpp's user avatar
  • 371
2 votes
0 answers
262 views

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? ...
mmpp's user avatar
  • 371
2 votes
1 answer
767 views

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: ...
mmpp's user avatar
  • 371
1 vote
0 answers
17 views

Is it possible to do cell composition for scATAC-seq data without scRNA-seq data?

Background My understanding was that if I did scATAC-seq and I have some clusters of cell groups, the only way I can label it is by correlating those groups with scRNA-seq data. My lab ordered some ...
Jonathan's user avatar
  • 341
4 votes
2 answers
96 views

Arrange ggplot Figure for scRNA-seq data

I have generated a ggplot for 8 single-cell libraries, with the purpose of visualizing the tSNE facet plot by sample, colored by cell type -- with percentages. The best I could get to is this - ...
ShaniS's user avatar
  • 51
0 votes
1 answer
98 views

How to solve correlation problems between different samples in scRNA-seq?

I am trying to align and merge different samples from NCBI. I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 ...
Alexis Finkbeiner's user avatar
0 votes
1 answer
46 views

Is use_dimred deprecated or is this a runTSNE() bug?

NOTE: I posted the same question on Biostars but so far no replies there so I figured I would ask here, too. So, I was running a pipeline which I developed some time ago and a very weird behaviour was ...
gabt's user avatar
  • 330
1 vote
1 answer
48 views

(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 ...
Angus Campbell's user avatar
2 votes
2 answers
1k views

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' ...
Zizogolu's user avatar
  • 2,148
1 vote
2 answers
773 views

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 ...
ShaniS's user avatar
  • 51
2 votes
3 answers
4k views

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 ...
Shani's user avatar
  • 21