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Seurat object missing after running PCA · Issue

Seurat object missing after running PCA · Issue

Seurat object missing after running PCA · Issue #8219 - GitHub

Hi all, I've just updated my Seurat from V4 to V5 and found that my Seurat object was missing after RunPCA. Here's my object before running ...

Error while running PCA on 1.3 Million Brain Cells from E18 Mice

If I use the randomly sampled 20k cells generated by 10X I do not have any problem creating the Seurat object. Can someone please let me know ...

Can't do runPCA after merging a splited Seurat object before UMAP

Hi,. The error message is quite clear, you need to do one of two things: Run FindVariableFeatures(). Or. provide a vector of feature names.

Run Principal Component Analysis — RunPCA • Seurat - Satija Lab

Run a PCA dimensionality reduction. For details about stored PCA ... Returns Seurat object with the PCA calculation stored in the reductions slot ...

RunUMAP code error after merged spatial transcriptomic objects

any thoughts on what happened and how to overcome this? tried to check packages update them but did not work. pca · seurat.

runPCA error / Error in runSVD(x, k = rank, nu = ifelse(get.pcs, rank ...

You probably want to runPCA on a SingleCellExperiment object, not a list with fields data and labels . The example you posted is using ...

Why do authors never attach their Single Cell analysis structure to ...

It's just storage and hosting issues. A Seurat object can get very large very quick so the authors need to figure out a storage online, which ...

active.ident slot present but not recognized in seurat object - Biostars

I get the same error when I try to visualize the active.ident in the four initial seurat objects that I used to create the merged.sct, so my ...

Seurat.utils | Various utility functions for Seurat single-cell analysis

Applies a series of Seurat processing steps to each Seurat object in a list. The operations include scaling data, running PCA, UMAP, finding neighbors, and ...

Analysis, visualization, and integration of spatial datasets with Seurat

This reads in the output of the spaceranger pipeline, and returns a Seurat object that contains both the spot-level expression data along with ...

seurat - Using external list of PCs for clustering

Try str(seuset) to ensure your Seurat object is whole. You might also RunPCA() within Seurat and return to cell.embeddings to ensure the format ...

SeuratObject.pdf

BugReports https://github.com/satijalab/seurat-object/issues ... Description. Pull information on previously run commands in the Seurat object.

Single-cell RNA-seq clustering analysis: Integration - GitHub Pages

If we had performed the normalization on both conditions together in a Seurat object ... Let's start with PCA. # Run PCA seurat_integrated <- RunPCA(object ...

Seurat Tutorial - 65k PBMCs - Parse Biosciences Support Suite

When we create our Seurat object the plate well numbers (column names in ... These will be used in downstream analysis, like PCA. pbmc ...

satijalab/seurat source: R/dimensional_reduction.R - rdrr.io

... (object = object[['pca']], slot = 'empirical') #' represents p-values for each gene in the PCA analysis. If ProjectPCA is #' subsequently run, JS(object = object ...

DittoDimPlot errror: Cannot find 'NA' in this Seurat object

I aim to use dittoSeq for visualizations, however, I am facing a problem regarding NA values. The batches are saved in the metadata slot of my ...

Seurat Example - Babraham Bioinformatics

We can find the gene names as the rownames of the Seurat object and we identify the mitochondrial genes by their names starting with “MT-”. Be aware that in ...

FindVariableFeatures Function in Seurat Producing "Error in match ...

I am running Seurat V3 in RStudio and attempting to run PCA on a newly subsetted object. As part of that process, I am using the commands ...

Seurat.pdf

Returns Seurat object with the PCA calculation stored in the reductions slot. RunSLSI. Run Supervised Latent Semantic Indexing. Description. Run ...

SeuratObject source: R/seurat.R - rdrr.io

The Seurat object is a representation of single-cell expression data for R; each Seurat object revolves around a set of cells and consists of one or more \code ...