Unclear what IntegrateLayers

Unclear what IntegrateLayers (v5) is actually doing vs IntegrateData ...

The integration workflow in v5 is streamlined from a code/usability perspective, but the steps are the same as the workflow you paste above.

Error with IntegrateLayers · Issue #9366 · satijalab/seurat - GitHub

Enterprise-grade 24/7 support · Pricing. Search or jump to... Search code, repositories, users, issues, pull requests... Search. Clear.

Introduction to scRNA-seq integration Seurat - Satija Lab

Integration of single-cell sequencing datasets, for example across experimental batches, donors, or conditions, is often an important step in ...

Seurat v5 integration -- question on "SCT" vs "integrated" assay

So now I am confused…. and I guess my main question is: When I plot features from the SCT assay, am I looking at data that is specific to the ...

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

When we compare the similarity between the ctrl and stim clusters in the above plot with what we see using the the unintegrated dataset, it is clear that this ...

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

Find a set of anchors between a list of \code{\link{Seurat}} objects. These anchors can later be used to integrate the objects using the \code{\link{ ...

Integration Seurat different healthy samples (fresh vs frozen) - Biostars

7 of them were frozen samples and S8 in the umap plot is the only fresh sample. So we can see a clear batch effect between S8 and all the other ...

9 scRNA-seq Dataset Integration

UMAP plot of the datasets before integration shows clear separation. Note that we can use patchwork syntax with Seurat plotting functions: DimPlot ...

Analysis, visualization, and integration of spatial datasets with Seurat

... integration of spatial and molecular information. ... This strategy works will in this case, as the clusters above exhibit clear spatial ...

12. Data integration - Single-cell best practices

Often when looking at these plots you will see a clear separation between batches. In this case, what we see is more subtle and while cells from ...

Single-cell RNA-seq: Performing Integration - GitHub Pages

When we compare the similarity between the ctrl and stim clusters in the above plot with what we see using the the unintegrated dataset, it is clear that this ...

Embedding number for visualization - scvi-tools - scverse Discourse

Recently I found some standard deviation (sd) of embedding scores after scvi integration were closed to 0 (about 0.02, the information was ...

Tuning seurat integration strength to prevent overcorrection - Biostars

You need to clarify which type of integration you are performing (rPCA or CCA?). If it is rPCA, you can tweak the k.anchor argument.

Removing cell cycle genes in large data set integration

The "linear model based cell cycle correction" page was updated a month ago, that confused me which opinion is more recent. Without digressing ...

Protocols for single-cell RNA-seq and spatial gene expression ...

This protocol demonstrates how to perform integration of Visium spatial gene expression data with single-cell RNA-seq data using two tools: ...

What is an Integration Layer? - Klipfolio

Before you start, take inventory of your data systems. Check where all your information is coming from and where it needs to go. This step helps you get a clear ...

Seurat Integration - single cell - Bioinformatics Stack Exchange

Are you using the same data from the integration tutorial or using your own data? How many cells/genes are in your dataset?

Paired single-cell multi-omics data integration with Mowgli - Nature

Integrative Matrix Factorization (integrative MF) and variational ... clear one-to-one associations between factors and cell types. In ...

Integrating data using ingest and BBKNN - Scanpy tutorials

... integration [Butler2018,Haghverdi2018] and many times ever since. ... 13. t_cell, 7. MHC class II, 5. unclear, 4. unclassified, 2. To simplify ...

Multiplex methods provide effective integration of multi-omic data in ...

... matrix of environmental conditions in two different layers: transcriptomics and fluxomics. ... clear scarcity of conditions in the high byproduct, low biomass ...