Using sctransform in Seurat

Using Seurat with multimodal data · Seurat - Guided Clustering Tutorial · Introduction to SCTransform, v2 regularization · Using sctransform in Seurat · Sketch ...

Tips for integrating large datasets • Seurat - Satija Lab

Create a list of Seurat objects to integrate · Perform normalization, feature selection, and scaling separately for each dataset · Run PCA on each ...

Update pre-V4 Assays generated with SCTransform in the Seurat to ...

Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay class · Arguments · Value · Contents.

Sketch-based analysis in Seurat v5 - Satija Lab

We store sketched cells (in-memory) and the full dataset (on-disk) as two assays in the same Seurat object. Users can then easily switch between ...

Seurat - Satija Lab

Fix issue with leiden option for FindClusters; Fix for data transfer when using sctransform; SDMTools moved to Suggests as package is orphaned. Seurat 3.1.2 ...

Merge SCTAssay objects - Seurat - Satija Lab

SCTransform, v2 regularization · Using Seurat with multi-modal data · Seurat v5 ... A single Seurat object or a list of Seurat objects. add.cell.ids. A ...

Transfer data — TransferData • Seurat - Satija Lab

SCTransform, v2 regularization · Using Seurat with multi-modal data · Seurat v5 ... Sketch integration using a 1 million cell dataset from Parse Biosciences ...

Installation Instructions for Seurat - Satija Lab

Seurat v5: Seurat 5: Install from GitHub · SeuratData: automatically load datasets pre-packaged as Seurat objects · Azimuth: local annotation of scRNA-seq and ...

Seurat - Dictionary Learning for cross-modality integration - Satija Lab

We normalize gene expression data using sctransform, and ATAC data using TF-IDF. # normalize multiome RNA DefaultAssay(obj.multi) < ...

Data visualization methods in Seurat - Satija Lab

We have found this particularly useful for small clusters that do not always separate using unbiased clustering, but which look tantalizingly ...

Calculate the percentage of all counts that belong to a given set of ...

SCTransform, v2 regularization · Using Seurat with multi-modal data · Seurat v5 Command Cheat Sheet; Data Integration; Introduction to scRNA-seq integration ...

Demultiplexing with hashtag oligos (HTOs) - Satija Lab

12-HTO dataset from four human cell lines · Create Seurat object, add HTO data and perform normalization · Demultiplex data · Visualize ...

Calculate module scores for feature expression programs in single ...

SCTransform, v2 regularization · Using Seurat with multi-modal data · Seurat v5 Command Cheat Sheet; Data Integration; Introduction to scRNA-seq integration ...

Seurat Command List - Satija Lab

Since Seurat v3.0, we've made improvements to the Seurat object, and added new methods for user interaction. We also introduce simple functions ...

Select integration features — SelectIntegrationFeatures - Satija Lab

Using Seurat with multi-modal data · Seurat v5 Command Cheat Sheet; Data ... SCTransform normalization pancreas.list <- lapply(X = pancreas.list, FUN ...

Sketch integration using a 1 million cell dataset from Parse ...

We create a Seurat object for this dataset. Since the input to CreateSeuratObject is a BPCells matrix, the data remains on-disk and is not ...

Find integration anchors — FindIntegrationAnchors • Seurat

Find a set of anchors between a list of Seurat objects. These anchors can later be used to integrate the objects using the IntegrateData function.

Feature expression heatmap — DoHeatmap • Seurat - Satija Lab

PBMC 3K guided tutorial · Data visualization vignette · SCTransform, v2 regularization · Using Seurat with multi-modal data · Seurat v5 Command Cheat Sheet ...

Seurat - Interaction Tips - Satija Lab

This vignette demonstrates some useful features for interacting with the Seurat object. For demonstration purposes, we will be using the 2,700 PBMC object that ...

Map COVID PBMC datasets to a healthy reference - Satija Lab

We aggregate all cells within the same cell type and donor using the AggregateExpression function. This returns a Seurat object where each 'cell ...