Seurat subset function. Integration Functions related to the Seurat v3 integration and label transfer algorithms Creates a Seurat object containing only a subset of the cells in the original object. Throughout this tutorial we will Apply quality control parameters to retain only high quality cells Normalize and scale the data Mar 9, 2018 · Hi Seurat team, I just started using Seurat about 2 weeks ago and I find it really powerful and user friendly. The integrated assay consists of 3000 features comings from Aug 20, 2025 · We update the Seurat infrastructure to enable the analysis, visualization, and exploration of these exciting datasets. names, low. Yesterday I updated my R from 4. Here’s a step-by-step guide on how to execute this process: Jun 10, 2024 · This guide will walk you through the concept of Seurat Subset, explaining its importance and demonstrating how to effectively use it in your research. 22 merge_seurat_metadata() Mar 29, 2023 · I have a Seurat object in which the meta. However, you may have already identified an issue here. This works the same way as for standard Assay objects. rds file in a specified directory. Jan 30, 2023 · To solve this I have changed the name of the genes when loading the matrices before creating the seurat object, this way the genes have the same name in all the object and there are no inconsistencies in the subsequent analysis. You can then create a vector of cells including the sampled cells and the remaining cells, then subset your Seurat object using SubsetData() and compute the variable genes on this new Seurat object. Jun 26, 2023 · After updating R studio, Seurat subset() function doesn't work. These genes can then be used for dimensional reduction on the original data including all cells. We start by reading in the data. By providing a clear and concise representation of gene expression patterns across cell clusters, the Dotplot Seurat helps researchers gain insights into cellular functions, identify marker genes, and compare cell populations. Clustering is a critical step in the single-cell analysis workflow, occurring after dimensionality reduction and before differential expression analysis. Value x with just the cells and features specified by cells and features for the layers specified by layers Mar 19, 2022 · I have a Seurat object that I have run through doubletFinder. In the previous step, we applied the filtering criteria directly using the subset function. null = FALSE, ) # S3 method for class 'Seurat' x[i, j, ] To create a subset of a Seurat object based on orig. by and subset. For a specific purpose, I do not want to create a new object but would like to filter out some low distributed features in the down-stream analysis. We are excited to release Seurat v5! This updates introduces new functionality for spatial, multimodal, and scalable single-cell analysis. data based on orig. For each replicate assign a unique FOV for easier downstream processing: Dec 27, 2020 · 在单细胞数据分析中，在确定细胞类型后，除了可以进行差异表达基因分析外，还可以针对单个细胞类型进行分析特定分析，这时就需要我们提取细胞子集分开处理了。一、Seurat数据格式 reverse Reverse ordering afxn Function to evaluate each identity class based on; default is mean reorder. Jan 8, 2022 · I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. CD4+ Helper T cells). Seurat. This is related to subsetting on multiple values of a discrete metadata field, in the case someone (accidentally o Other correction methods are not recommended, as Seurat pre-filters genes using the arguments above, reducing the number of tests performed. To perform hierarchical clustering several linkage functions are available, including single, complete, and Ward. data before using the subset () function but that didn't work Jan 23, 2024 · Dear Seurat team. warn. 1). Oct 16, 2019 · How to subset () or exclude based on cell ID/name (ex. thresholds, high. Mar 29, 2023 · To gain full voting privileges, How to get subset of a Seurat object based on metadata? I have a Seurat object in which the meta. vlnplot. To perform the subclustering, there are a couple of different methods you could try. Is there a way to do that? I just do not want to do manual subsetting on 10 genes, then manually getting @data matrix from each subset, and recreating seurat object afterwards. How can I remove doublets from this and which assay should I use "RNA", "SC Jul 24, 2019 · Hi all, I'm also interested to this topic: what is the best way to subset and reclustering data starting from an integrating dataset? After subsetting clusters of interest (subsetting by ident) I have a Seurat object with RNA, SCT and integrated assay, and dimensional reduction (pca, tsne, umap) coming from the original Seurat object. Interestingly, we’ve found that when using sctransform, we often benefit by pushing this parameter even higher. We will be adding support for additional imaging-based technologies in the coming months. For more details about progressr, please read vignette ("progressr-intro") Perform default differential expression tests The bulk of Seurat’s differential expression features can be accessed through the FindMarkers () function. With Seurat, you can easily switch between different assays at the single cell level (such as ADT counts from CITE-seq, or integrated/batch-corrected data). <p>Subset a Seurat object</p>Extra parameters passed to WhichCells, such as slot, invert, or downsample This enables us, for example, to subset the Seurat object by a particular trait or to remove cells with a particular characteristic, or do differential expression between cells of different cell types. 2. Lastly, as Aaron Lun has pointed out, p-values should be interpreted cautiously, as the genes used for clustering are the same genes tested for differential expression. I want to divide my data into two, one only have those two cells and another data without those two cells. Nov 9, 2023 · I was previously capable of manipulating this Seurat object with the subset function no without issue. Jan 4, 2024 · I have done this in the past with older versions of Seurat where I had applied the integration workflow that creates an assay slot called "integrated". i, features Depends on the method [, subset Feature names or indices $, $<- Name of a single metadata column [[, [[<- Name of one or more metadata columns or an associated object; associated objects include Assay, DimReduc, Graph, SeuratCommand, or SpatialImage objects Arguments passed to Jan 13, 2019 · Much like R's subset function, subset. Here, we integrate three of the objects into a reference (we will use the fourth later in this vignette as a query dataset to demonstrate mapping). Read in raw Xenium data using Seurat's LoadXenium() function. Please check the documentation of the function for more information (simply run ?Seurat::SubsetData in R). It can also happen, for example, when multiple datasets are merge d. Most functions now take an assay parameter, but you can set a Default Assay to avoid repetitive statements. Introduction and Learning Objectives This tutorial has been designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. Sep 3, 2021 · You can remove cells in a Seurat object using the subset() function, or the [ operator, for example Value A named list of Seurat objects, each containing a subset of cells from the original object. wilcox. Any suggestions? Contents Seurat-package AddAzimuthResults AddAzimuthScores AddModuleScore AggregateExpression AnchorSet-class AnnotateAnchors Assay-class AugmentPlot AutoPointSize AverageExpression BGTextColor BarcodeInflectionsPlot BlackAndWhite BridgeCellsRepresentation BridgeReferenceSet-class BuildClusterTree BuildNicheAssay CCAIntegration CalcDispersion CalcPerturbSig CalculateBarcodeInflections Merge Details When merging Seurat objects, the merge procedure will merge the Assay level counts and potentially the data slots (depending on the merge. use = NULL Dec 9, 2022 · I am trying to subset a seurat object obtained from CosMx's nanostring scRNA-seq dataset using the following code: CosMx_T <- subset(CosMx, idents = "Tumour") But it cluster3. We believe this is because the sctransform workflow performs more effective normalization, strongly removing technical Sep 2, 2021 · I have noticed some unexpected behavior for the subset function on Seurat objects. 1 and ident. use argument of the SubsetData() function from Seurat. I have a seurat object that I have subsetted out to include only clusters that have genes expressed in excitatory neurons. We clearly want to remove cells that were classified as doublets by both tools. To subset the dataset, Seurat has a handy subset() function; the identity of the cell type (s) can be used as input to extract the cells. I have problems with the subsetting of seurat objects after I create them from matrix, feature and barcode files: Oct 29, 2023 · Hi, I would like to know how to subset Xenium object. Also I was trying the LoadNanostring() function in V5 which is also very much not outputting the same object structure as for V4 which means all my previous code that was working 2 months ago are now with errors! Apr 24, 2025 · Clustering Relevant source files Purpose and Scope This document explains the clustering functionality in Seurat, which enables the identification of cell populations in single-cell datasets. x' and later update seurat to 'v. Mar 18, 2024 · I have tried several methods to filter the seurat object using the subset () function but I've been running into errors I tried adding the V1 column of the seurat object meta. This includes how to access certain information, handy tips, and visualization functions built into the package. 0) with Seurat 4. Make sure to set unique FOV names for each slice for easier downstream processing. But suddenly, many steps are getting messy due to the confusing layers. The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts. For posterity, the current workaround is to first subset any relevant SeuratObject s, and manipulate any spatial coordinates layers afterward. Learning Objectives Learn about options for analyzing your scRNA-Seq data. 2 parameters. 0, we’ve made improvements to the Seurat object, and added new methods for user interaction. PDF Getting Started with Seurat: Differential Expression and Classification 1. When I try to include multiple samples, it doesn’t work. 1 to 4. data parameter). data[["DF. 1) However, I want to subset on multiple genes. 0, I get an error. In this vignette, we focus on three datasets produced by different multiplexed imaging technologies, each of which is publicly available. Seurat Cheatsheet This cheatsheet is meant to provide examples of the various functions available in Seurat. If updating the package and object doesn't solve the issue then it would seem like there might be an issue with your specific object. ident should work. Oct 30, 2019 · Seurat::subset() doesn't accept soft-coded parameters inside a function. The PercentageFeatureSet() will take a pattern and search the gene identifiers. Usage SplitObject(object, split. by parameter). use parameter (see our DE vignette for details). The Read10X() function reads in the output of the cellranger pipeline from 10X, returning a Mar 29, 2023 · How to get subset of a Seurat object based on metadata? Jul 1, 2024 · Hi, This is a follow up on issue #8362. Jul 2, 2024 · filtered_seurat <- subset(filtered_seurat, features = keep. Only matching names are returned. Oct 31, 2023 · Setup the Seurat Object For this tutorial, we will be analyzing the a dataset of Peripheral Blood Mononuclear Cells (PBMC) freely available from 10X Genomics. 54K subscribers Subscribed I want to create a subset of a cell expressing certain genes only. 1. We will start with a merged Seurat Object with multiple data layers representing multiple samples. I want to subset from my original seurat object (BC3) meta. When you subset a Seurat object with multiple layers and end up with one of the samples represented by only one cell, you can no longer subset the object any In the standard Seurat workflow we focus on 10 PCs for this dataset, though we highlight that the results are similar with higher settings for this parameter. seurat. In Seurat v5, we introduce new infrastructure and methods to analyze, interpret, and explore these exciting datasets. Description Subset Seurat Objects Usage ## S3 method for class 'Seurat' subset( x, subset, cells = NULL, features = NULL, idents = NULL, return. classification Mar 27, 2023 · subset (pbmc, subset =replicate=="rep2") ## An object of class Seurat ## 13714 features across 1290 samples within 1 assay ## Active assay: RNA (13714 features, 2000 variable features)## 2 dimensional reductions calculated: pca, umap # Can I create a Seurat object of just the NK cells and B cells? subset (pbmc, idents = c ("NK", "B")) Chapter 3 Analysis Using Seurat The contents in this chapter are adapted from Seurat - Guided Clustering Tutorial with little modification. obj using the tutorial codes. Aug 28, 2025 · subset. The results of hierarchical clustering are visualized by a reordered heatmap together with the resulting dendrograms. Seurat: Subset 'Seurat' Objects In SeuratObject: Data Structures for Single Cell Data View source: R/seurat. numeric Rename all identity classes to be increasing numbers starting from 1 (default is FALSE) x, object Jan 31, 2018 · Hi, The way to proceed is to first create a character vector of cell names for each expected cell type in the dataset, and then pass these vectors sequentially to the cells. I'm trying to get the subset function in Seurat to subset based on the expression level of one of these without referring to the actual gene name in the function. 6 and pbmc3k object with no errors. ident, researchers can utilize the subset() function provided within the package. it throws an error to the code I have used before and worked fine The FindMarkers() function in the Seurat package is used to perform differential expression analysis between groups of cells. The SpatialFeaturePlot () function in Seurat extends FeaturePlot (), and can overlay molecular data on top of tissue histology. SubsetRow: Return a subset of rows for a matrix or data frame Description Return a subset of rows for a matrix or data frame Usage SubsetRow(data, code, invert = FALSE) Arguments Aug 18, 2021 · The function of "CreateSeuratObject" filters out low quality of cells and features from the raw data set. 3. (for example, cluster 9 shows both NK and CD4 cells) How can I split a cluste The function makes groups based on the metadata columns we specify, sums the counts for each gene within the group, and then log normalizes and scales the data. Have you tried updating to current version of Seurat (if possible)? I have run the following code with Seurat 4. the Crop function. Note that for large data sets with diverse samples, it may be beneficial to use sample-specific thresholds for some parameters. null = FALSE Jul 25, 2023 · We read every piece of feedback, and take your input very seriously PDF Getting Started with Seurat: QC to Clustering Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. Learn about resources for learning R programming. In this tutorial, we will learn how to Read 10X sequencing data and change it into a seurat object, QC and selecting cells for further analysis, Normalizing the data, Identification of Nov 7, 2024 · On other Seurat functions it will default to counts if the data layer is not present, so I wasn't sure how to grab what I wanted. The merge will optionally merge reductions depending on the values passed May 18, 2020 · Best, Sam Hi Nitin, You can use the subset function and specify the idents of the clusters to keep (or remove if you set invert = TRUE) and that will remove the cells in those clusters. Nov 8, 2019 · I'm recently running into issues with the subset function on scRNA-seq multiple datasets. Here is my coding but it always shows 'No named arguments passed' I have no idea how to correct that. data before using the subset () function but that didn't work Jun 8, 2025 · RunUMAP: Run UMAP In Seurat: Tools for Single Cell Genomics View source: R/generics. obj_combined_filtered_excitatiory <- subset Arguments object An object x, y Range to crop x/y limits to; if NULL, uses full range of x / y coords Coordinate system to execute crop; choose from: “ plot ”: Coordinates as shown when plotting “ tissue ”: Coordinates from GetTissueCoordinates Arguments passed to other methods Sep 27, 2023 · 0 or anyone familiar with Seurat: How would I subset an integrated seurat object down to multiple samples? I was able to subset an object to 1 sample using 1 of the the group IDs as shown below. I've received multiple different Dec 12, 2017 · Hi, I guess you can randomly sample your cells from that cluster using sample() (from the base in R). Mar 27, 2023 · In Seurat v2 we also use the ScaleData () function to remove unwanted sources of variation from a single-cell dataset. 1'. 2 the two groups of cells we are interested in comparing. by = "ident") Value A named list of Seurat objects, each containing a subset of cells from the original object. I have a well established pipeline that was runing well two weeks ago. A Seurat has a convenient function that allows us to calculate the proportion of transcripts mapping to mitochondrial genes. limma. 3M E18 mouse neurons (stored on-disk), which we constructed as described in the BPCells vignette. We will start with a merged Seurat Object with multiple data layers representing multiple samples that have already been filtered and undergone preliminary clustering Aug 18, 2018 · I have a SC dataset w 22 clusters and want to use DotPlot to show Hox complex expression. There are 2,700 single cells that were sequenced on the Illumina NextSeq 500. Jul 17, 2024 · Hi everyone! Now I am struggling with a couple of issues related to Seurat v5. With Seurat, all plotting functions return ggplot2-based plots by default, allowing one to easily capture and manipulate plots just like any other ggplot2-based plot. The distance measures and linkage functions for clustering genes and samples can be chosen independently. Best, Sam To identify these cell subsets, we would subset the dataset to the cell type (s) of interest (e. Sep 15, 2020 · For the purpose of extracting all "neigbour" spots for a cluster of interest, I would prefer to use the spot row and column coordinates. ident. Jun 17, 2025 · Gene expression visualization In Seurat, we have functionality to explore and interact with the inherently visual nature of spatial data. PDF Introduction to scRNA-Seq with R (Seurat) This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. 5)# Subset on a combination of criteria subset (x =pbmc, subset =MS4A1>2. Nov 25, 2022 · Hello, I have a question about version of seurat and subset function. The STARmap class Subset an AnchorSet object Subset a Seurat Object based on the Barcode Distribution Inflection Points Find cells with highest scores for a given dimensional reduction technique Find features with highest scores for a given dimensional reduction technique Get nearest neighbors for given cell The TransferAnchorSet Class Transfer Oct 31, 2023 · Here, we describe important commands and functions to store, access, and process data using Seurat v5. After updating the seurat, subset function does not w Other correction methods are not recommended, as Seurat pre-filters genes using the arguments above, reducing the number of tests performed. 4) and Seurat (4. For examples I want to extract Endothelial from complex cells data. The data we used is a 10k PBMC data getting from 10x Genomics website. Are there any suggestions to do so? Is that Arguments x, object A Seurat object pattern A regular expression. Seurat is designed for interactive use only. 0. To enable progress updates, wrap the function call in with_progress or run handlers (global = TRUE) before running this function. Jan 23, 2021 · Hello - this might be a ore generic R question than seurat, but perhaps you might know. p_A. Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on. For example, we could ‘regress out’ heterogeneity associated with (for example) cell cycle stage, or mitochondrial contamination i. Apr 23, 2019 · Hi, Using group. Jun 16, 2023 · This is not limited to modifying via. The code here also removes cells with zero counts, and saves data as . obj, selection. Oct 31, 2023 · In Seurat, we also use the ScaleData () function to remove unwanted sources of variation from a single-cell dataset. features) Additionally, I have a general question: how should one handle analysis with multiple layers when performing filters, assigning cell cycle scores, and identifying/removing doublets? Nov 10, 2023 · Merging Two Seurat Objects merge () merges the raw count matrices of two Seurat objects and creates a new Seurat object with the resulting combined raw count matrix. pos <- Idents(my Nov 30, 2023 · Problem was solved by downgrading packages Matrix (1. I am trying to subset the object based on cells being classified as a 'Singlet' under seurat_object@meta. Learn how to import your data for working with R. The resulting object is structured like our single-cell Seurat object with different layers for the raw counts (counts), log normalized (data) and scaled (scale. Feb 8, 2022 · Hi, Not member of dev team but hopefully can be helpful. Arguments x A Seurat object subset Logical expression indicating features/variables to keep cells, j A vector of cell names or indices to keep features, i A vector of feature names or indices to keep idents A vector of identity classes to keep return. Dbh. 4. 4 == 0) I have a situation where I am try We can do this really easily with the function subset (), which is part of the Seurat package, to just keep cells that are marked as singlet. Usage FilterCells(object, subset. Usage WhichCells(object, ) # S3 method for Assay WhichCells(object, cells = NULL, expression, invert = FALSE, ) # S3 method for Seurat WhichCells( object, cells = NULL, idents = NULL, expression Seurat Video Tutorials--Video 12: The Subset Function Single Cell Genomics, Transcriptomics & Proteomics 3. Jan 17, 2024 · To integrate the two datasets, we use the FindIntegrationAnchors () function, which takes a list of Seurat objects as input, and use these anchors to integrate the two datasets together with IntegrateData (). When I reclustered a subset of cells I set DefaultAssay (object) <- "integrated" and then proceeded with remaining clustering functions (RunPCA, FindNeighbors, FindClusters, RunUMAP). I create a Assay object 'Baiting' to my seurat object 'cell', and I run the 'subset' command to filter the cell/gene. The Qs are a) how to plot clusters in order of my choosing, b) how to plot a specific subset of clusters. R Apr 23, 2023 · Seurat V5 completely screwed up the subsetting for me too. obj <- FindVariableFeatures(cluster3. i made seurat object with 'v. Thumbs up for the great work! I wanted to ask how can I subset a group of cells expressing only a certain gene? For example, f Mar 19, 2024 · I have tried several methods to filter the seurat object using the subset () function but I've been running into errors I tried adding the V1 column of the seurat object meta. Follow a step-by-step standard pipeline for scRNAseq pre-processing using the R package Seurat, including filtering, normalisation, scaling, PCA and more! Seurat v5 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC. While we currently don't offer a programmatic way to subset Seurat objects based on feature expression, this can be accomplished relatively easily using which and FetchData Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. These functions ensure compatibility with older versions of the Seurat package and may be removed in future updates. Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate. By default, Seurat performs differential expression (DE) testing based on the non-parametric Wilcoxon rank sum test. May 24, 2019 · Creates a Seurat object containing only a subset of the cells in the original object. g. For example, the ROC test returns the ‘classification power’ for any individual marker (ranging from 0 - random, to 1 - perfect). Rfast2. 6-1. : I am pretty new to Seurat. Mar 27, 2023 · Since Seurat v3. . msg Show message about more efficient Moran's I function available via the Rfast2 package Seurat. I know that I can do subsetting on just one gene in Seurat: seurat_subset <- SubsetData(seurat_object, subset. data include a column name "predicted_cell_type". null If no cells are requested, return a NULL; by default, throws an error Arguments passed # S3 method for class 'Seurat' subset( x, subset, cells = NULL, features = NULL, idents = NULL, return. method = "vst", nfeatures = 2000) Now I am wondering, how do I extract a data frame or matrix of this Seurat object with the built in function or would I have to do it in a "homemade"-R-way? I'm hoping it's something as simple as doing this: Intro: Sketch-based analysis in Seurat v5 As single-cell sequencing technologies continue to improve in scalability in throughput, the generation of datasets spanning a million or more cells is becoming increasingly routine. 3 Algorithm and implementation Now, filter the data using the subset function and your chosen thresholds. Since we want the ratio value Jun 14, 2024 · Conclusion The Dotplot Seurat is a valuable tool for visualizing and interpreting scRNA-seq data. 5&PC_1>5) subset (x Explore the power of single-cell RNA-seq analysis with Seurat v5 in this hands-on tutorial, guiding you through data preprocessing, clustering, and visualization in R. Jul 15, 2020 · How can I remover doublet in a subset of Seurat object?. name = neuron_ids[1], accept. Graphs the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique. We provide arguments to specify ident. I use subset function to generate a smaller seurat object from SCTransform integrated big seurat object. e. Following the tutorial "Analysis of Image-based Spatial Data in Seurat", I cropped xenium. seurat. It will also merge the cell-level meta data that was stored with each object and preserve the cell identities that were active in the objects pre-merge. One can subset a seurat object with an expression like this: x <- subset (seuratObj, subset = ClusterNames_0. Based on the code you provided, it looks like you're pulling the cell names (barcodes) from an object called seurat_obj where as you're running FindMarkers on an object called combined? If these are actually different objects, that would explain the difference in DE results between your two methods. 2 and updated to Seurat V5. Learn about Seurat and the Seurat object including how to create the Integration Functions related to the Seurat v3 integration and label transfer algorithms Package index • SeuratObjectContents Aug 21, 2025 · Subsetting a ChromatinAssay We can use the standard subset () function or the [ operator to subset Seurat object containing ChromatinAssay s. I believe it is a bug, as I'm successful at subsetting the same Seurat object on a Docker image of Seurat and at earlier times in the same Seurat session in my personal Macbook. The values of this column include "0:CD8 T cell", "1:CD4 T cell", "2:spinous cell", etc. The calculation here is simply Mar 27, 2023 · Integration of 3 pancreatic islet cell datasets Next, we identify anchors using the FindIntegrationAnchors () function, which takes a list of Seurat objects as input. Briefly, nesting divides tables into subsets according to any reference column, while the map function allows applying operations across subsets iteratively. May 20, 2019 · Hi Seurat team : My question is whats the difference between "SubsetData" and "subset" function. To demonstrate commamnds, we use a dataset of 3,000 PBMC (stored in-memory), and a dataset of 1. This is useful when trying to compute the percentage of transcripts that map to mitochondrial genes for example. Creates a Seurat object containing only a subset of the cells in the original object. Reprex This function enables you to easily calculate the percentage of all the counts belonging to a subset of the possible features for each cell. FilterCells: Return a subset of the Seurat object Description Creates a Seurat object containing only a subset of the cells in the original object. With the following exact code, I could subset B cells successfully from same Jun 18, 2024 · Hello, I have a question about how I can find all cells that have at least one read mapped to any of these 8 activity-dependent genes: OSTN, BDNF, FOS, NPAS4, EGR1, LINC00473, ZNF331, PER1 using the Seurat R package. split Show message about changes to default behavior of split/multi violin plots Dec 9, 2020 · The Seurat PBMC tutorial makes use of the function DoHeatmap for visualizing the top n genes per cluster in a single figure. however, when i use subset (), it returns with Error. Jul 12, 2021 · Hi, I am using the subset function from Seurat to filter the genes present in the Seurat object as follows: sample <- subset (sample, features = keep) Aug 22, 2024 · Step 4: Filter the Cells After setting the filtering criteria, the next step in how to filter cells in Seurat scRNA analysis is to apply these criteria to remove unwanted cells from your dataset. The raw data can be found here. It looks like both you and @rharao confirmed that I can use slot = "counts" after switching my assay to RNA in order to subset based on raw counts, and then switching back to SCT on the main object. 1), SeuratObject (4. I would probably proceed as follows (if possible): Subset the cluster of interest to a separate Seurat object Extract barcodes and coordinates from this Seurat object Seurat has several tests for differential expression which can be set with the test. We also introduce simple functions for common tasks, like subsetting and merging, that mirror standard R functions. cropped. For each column (cell) it will take the sum of the counts slot for features belonging to the set, divide by the column sum for all features and multiply by 100. data) data. msg Show message about more efficient Wilcoxon Rank Sum test available via the limma package Seurat. I'm attempting to deliver a Seurat pipeline via a Java web-server so I would like to create a function that allows the user to make choices on normalizing/scaling their data based upon the QC visualization they see. By default, cells are colored by their identity class (can be changed with the group. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. low = 0. : WhichCells: Identify cells matching certain criteria Description Returns a list of cells that match a particular set of criteria such as identity class, high/low values for particular PCs, ect. To test for DE genes between two specific groups of cells, specify the ident. Apr 13, 2020 · There is a function is package Seurat called 'subset' which will subset a group from the dataset based on the expression level of a specific gene. coords <- Crop( Progress Updates with progressr This function uses progressr to render status updates and progress bars. <- subset (x = p, idents = c ("A"), invert = FALSE Jun 17, 2025 · Gene expression visualization In Seurat, we have functionality to explore and interact with the inherently visual nature of spatial data. cells Subset of cell names expression A predicate expression for feature/variable expression, can evaluate anything that can be pulled by FetchData; please note, you may need to wrap feature names in backticks (``) if dashes between numbers are present in the feature name invert Invert the selection of cells idents A vector of identity classes Finds markers (differentially expressed genes) for each of the identity classes in a dataset Learn how to efficiently subset a Seurat object in R based on metadata frequency, aimed at enhancing data analysis in single-cell RNA sequencing. PercentageFeatureSet: Calculate the percentage of all counts that belong to a given set of features Description This function enables you to easily calculate the percentage of all the counts belonging to a subset of the possible features for each cell. The weird thing is that t # Subset Seurat object based on identity class, also see ?SubsetData subset (x =pbmc, idents ="B") subset (x =pbmc, idents = c ("Naive CD4 T", "CD8 T"), invert =TRUE)# Subset on the expression level of a gene/feature subset (x =pbmc, subset =MS4A1>2. Feb 20, 2024 · Hi, I meet a problem when I use subset function. For example, we could ‘regress out’ heterogeneity associated with (for example) cell cycle stage, or mitochondrial contamination. thresholds, cells. This method works well for a few thousand cells, but loses resolution as the number of cells increase because individual columns have to be interpolated. "AAACCCAAGCATCAGG_1" and "AAACCCACAAGAGATT_1"). Oct 24, 2024 · This function samples a specified percentage of a dataframe (specifically a subset of the metadata of a Seurat object) and returns the corresponding cell IDs. You can directly use the gene name in the function like this which works fine: For example, useful for taking an object that contains cells from many patients, and subdividing it into patient-specific objects. The primary purpose of clustering is to group . R Mar 1, 2022 · If I try to subset an object (version 4. dqufl hkgjl ewqyapqz lwvjabx dnqsj lhr wtoagmw gbqll kvmpgh dirw

Seurat subset function. Aug 28, 2025 · subset.