integrating single|cell datasets

Introduction to scRNA-seq integration Seurat - Satija Lab

Introduction to scRNA-seq integration ... Integration of single-cell sequencing datasets, for example across experimental batches, donors, or ...

9 scRNA-seq Dataset Integration

There are two main approaches to comparing scRNASeq datasets. The first approach is “label-centric” which is focused on trying to identify equivalent cell-types ...

Integration of Single-Cell RNA-Seq Datasets

Multiple scRNA-seq datasets are often integrated and compared to check whether cellular features (e.g., cell subpopulations and their marker ...

Benchmarking atlas-level data integration in single-cell genomics

Single-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data ...

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

Integration is a powerful method that uses these shared sources of greatest variation to identify shared subpopulations across conditions or datasets [Stuart ...

12. Data integration - Single-cell best practices

Mutual nearest neighbors are pairs of cells from two different datasets which are in the neighborhood of each other when the datasets are placed ...

Population-level integration of single-cell datasets enables multi ...

The increasing generation of population-level single-cell atlases has the potential to link sample metadata with cellular data.

Integrating single-cell transcriptomic data across different conditions ...

Integrating single-cell transcriptomic data across different conditions, technologies, and species · Abstract. Computational single-cell RNA-seq (scRNA-seq) ...

SCIntRuler: guiding the integration of multiple single-cell RNA-seq ...

The purpose of data integration methods is to remove platform-specific or subject-specific batch effects. This is critical to prevent masking ...

Chapter 13 Integrating Datasets | Orchestrating Single-Cell Analysis ...

The function returns a SingleCellExperiment object containing corrected values for downstream analyses like clustering or visualization. Each column of mnn.out ...

integrating single-cell datasets - Swarup Lab

Constructs a shared embedding across datasets using an iterative approach in which cells are grouped using soft k-means clustering, and cluster centroids are ...

Chapter 6 Workflow: Integrating Datasets | Orchestrating Single-Cell ...

The multiBatchNorm() function from the scran package recomputes log-normalized expression values after adjusting the size factors for systematic differences in ...

iMAP: integration of multiple single-cell datasets by adversarial ...

The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and ...

Integrate single-cell RNA-Seq datasets in R using Seurat (CCA)

A detailed walk-through of steps to merge and integrate single-cell RNA sequencing datasets to correct for batch effect in R using the ...

Integrative analysis in Seurat v5 - Satija Lab

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

Comprehensive Integration of Single-Cell Data - ScienceDirect.com

The Seurat v3 anchoring procedure is designed to integrate diverse single-cell datasets across technologies and modalities. To facilitate the ...

Integrating single-cell datasets with ambiguous batch information by ...

Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features · To correct batch effects or technical variations ...

Integrating single-cell RNA-seq datasets with substantial batch effects.

We evaluated performance in three data settings, namely cross-species, organoid-tissue, and cell-nuclei integration. Cycle-consistency and VampPrior improved ...

15 Integrating single-cell 'omics datasets

Approaches for integrating single. Figure 15.1: Reproduction of Figure 6 from Laehnemann et al (2019). Approaches for integrating single-cell measurement ...

Comparing single-cell RNA integration methods | Which is the best?

Which single-cell integration method is the best? In this video I compare 5 different methods using 3 different challenging integration ...