seurat | R toolkit for single cell genomics | Genomics library

 by   satijalab R Version: v4.3.0 License: Non-SPDX

kandi X-RAY | seurat Summary

kandi X-RAY | seurat Summary

seurat is a R library typically used in Artificial Intelligence, Genomics applications. seurat has no bugs, it has no vulnerabilities and it has medium support. However seurat has a Non-SPDX License. You can download it from GitHub.

Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.

            kandi-support Support

              seurat has a medium active ecosystem.
              It has 1834 star(s) with 834 fork(s). There are 79 watchers for this library.
              It had no major release in the last 12 months.
              There are 281 open issues and 6069 have been closed. On average issues are closed in 13 days. There are 21 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of seurat is v4.3.0

            kandi-Quality Quality

              seurat has 0 bugs and 0 code smells.

            kandi-Security Security

              seurat has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              seurat code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              seurat has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              seurat releases are available to install and integrate.

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            seurat Key Features

            No Key Features are available at this moment for seurat.

            seurat Examples and Code Snippets

            No Code Snippets are available at this moment for seurat.

            Community Discussions


            ggplot2 overlapping causing issues with ridgeplot
            Asked 2022-Mar-23 at 14:50

            I am creating ridge plots from the Seurat package. This packages utilizes ggplot2. All of my ridge plots look great except for one. I am trying to manually adjust the bandwidth to make this plot look similar to the others but I wind up with two ridge plots overlapping one another.

            I can't post an example of the data as the data is a Seurat object and not a standard df. Apologies in advance!

            RidgePlot(object = sc1, features = "FGF2+Heparin") produces:

            When I attempt to change the bandwidth using + geom_density_ridges(scale = 2) I get this:

            I am trying to get it to look more similar to this:

            Thank you for your help!

            EDIT 02/23/22

            I have made good progress but I am still running into an issue. Ideally, ggplot2 would completely overwrite the previous points.



            Answered 2022-Mar-23 at 14:50

            I indirectly solved the issue I was having by changing the size of the bandwidth and the colors of the plots.

            I made some colors translucent so that you can see the peaks behind them. Example:

            This code applies to a single plot. p12 <- RidgePlot(sc1, features = "Y-27632") + geom_density_ridges2(scale = 4, bandwidth = 2.05) + theme(legend.position = "none") + xlab("Concentration [uM]") + ylab("Cluster") + scale_fill_manual( values = c("#FF3500A0", "#CC9933FF", "#33C04CCF", "#66CCFF", "#0000FF", "#FF66CC") )



            singularity container uses host libraries upon rendering .Rmd file
            Asked 2022-Mar-21 at 11:50

            I have build a singularity container based on r-base image and installing custom libraries like Seurat. Now I am trying to run my .Rmd script as follows:



            Answered 2022-Mar-21 at 11:50

            The $(...) statement is evaluated by bash and its output is what is sent to the singularity container. What you probably want is just:



            MongoDB unable to lookup docs based on variable parent document property
            Asked 2022-Feb-20 at 11:36

            I want to find products and for each product attach deals to it. A deal is a product from same collection, yet based on some common properties. So as per my requirement pipeline should return documents, for each document find other products those aren't same as current, but have equal detail.duration. But even though I've many docs with same duration, deals are always []. Could you please figure out the issue with my pipeline?

            Following is the aggregation pipeline I'm running: I've added filter _id $in just for clarity based on shown documents below. This isn't a part of real pipeline $match query.



            Answered 2022-Feb-20 at 11:36

            From $match (Restrictions)

            The $match query syntax is identical to the read operation query syntax; i.e. $match does not accept raw aggregation expressions. To include aggregation expression in $match, use a $expr query expression.

            And you need to use $$ to get the variable value.


            To reference variables in pipeline stages, use the "$$" syntax.

            Change the $match stage in the pipeline as:



            how to update R Rcpp to versions > 1.7
            Asked 2022-Feb-04 at 21:48

            I am trying to update Rcpp from 1.0.6 to 1.0.7 or 1.0.8. The Rcpp update is essential for a primary R library that I intend to use.

            I looked at the documentation and tried to install Rcpp using:



            Answered 2022-Feb-04 at 19:02

            So you are using Seurat. That is a big package with many recursive dependencies:



            Error adding and deleting characters from each element in a set of strings in R
            Asked 2022-Jan-02 at 08:34

            I'm trying to delete the first 7 characters of each string in a set of strings. I've been following akrun's wonderful answer here (how to add a character to a string in R). This is the command I've been using but it's returning an error:



            Answered 2022-Jan-02 at 08:34

            You could use substring, in combination with paste0. If you want to replace each string individually, use mapply, else sapply:



            Randomly subsampling seurat object
            Asked 2021-Nov-30 at 01:45

            I've been trying to randomly subsample my seurat object. I'm interested in subsampling based on 2 columns: condition and cell type. I have 5 conditions and 5 cell types. Main goal is to have 1000 cells for each cell type in each condition. I've tried this so far:

            First thing is subsetting my seurat object:



            Answered 2021-Nov-29 at 19:47

            I can't say for certain without seeing your data, but could you just add an if statement in the function? It looks like you're sampling column-wise, so check the number of columns. Just return x if the number of columns is less than the number you'd like to sample.



            Colour UMAP based on expression of multiple genes in ggplot2
            Asked 2021-Oct-17 at 23:08

            I was just wondering if anybody had any experience with coloring something like a UMAP made in ggplot based on the expression of multiple genes at the same time? What I want to do is something like the blend function in Seurat featureplots, but with 3 genes / colors instead of 2.

            I'm looking to make something like this:

            Where the colors for the genes combine where there is overlap.

            What I've gotten to so far is



            Answered 2021-Oct-17 at 23:08

            There is no 'vanilla' way of doing this in ggplot2. One can precalculate the blended colours and append invisible layers and scales with the ggnewscale package.

            Let's pretend for reproducibility purposes that we want to make a UMAP of the iris dataset and using the descriptors of leaves as 'genes'.



            subset data based on read counts for Seurat object (Error in FetchData)
            Asked 2021-Sep-09 at 22:07

            I'm trying to subset a Seurat object (called dNSC_cells) based on counts of genes of interest. Specifically, I have a list of genes and I plan on looping through them to subset my data and do some Wilcox tests. What I have so far looks like this:



            Answered 2021-Sep-09 at 22:07

            the subset function does not support gene symbol in variable, you need to extract a dataframe first.



            How to load Seurat Object into WGCNA Tutorial Format
            Asked 2021-Aug-22 at 23:27

            As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA ( I am really new to programming so it's probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA's tutorials (

            Here is what I have tried thus far:

            This tries to replicate datExpr and datTraits from part I.1:



            Answered 2021-Aug-22 at 23:27

            So doing as.matrix(datExpr) right after datExpr <- t(sobjwgcnamat)[,VariableFeatures(sobjwgcna)] worked. I had been trying it right before MEList = moduleEigengenes(datExpr, colors = moduleColors) and that didn't work. Seems simple but order matters I guess.



            How to use readRDS() in module with golem in shiny?
            Asked 2021-Aug-09 at 14:28

            Currently I am trying to read a rds-file inside of a module. I am using the golem package. This is my code right now and I don't know how to fix this.

            Goal: Once the rds-file is uploaded the conditionalPanel() should appear.

            Problem: Reading the file fails





            Answered 2021-Aug-09 at 14:28


            The problem was with readRDS(). I guess this is caused by the different namespacing when working with modules.


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install seurat

            You can download it from GitHub.


            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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