UMAP method- Dimensionality Reduction in Single Cell Genomics

by Xuan Nguyen | Mar 8, 2022 | All Blogs, Bioinformatics & single cell data analysis blogs

Dimension reduction methods – UMAPIn the previous blog, we introduced dimension reduction in single cell RNA-Sequencing (scRNA-Seq) as well as PCA and t-SNE dimension reduction methods. We have learned that single cell data are sparse, noisy, and...

Dimensionality Reduction in Single Cell Genomics

by Xuan Nguyen | Mar 8, 2022 | All Blogs, Bioinformatics & single cell data analysis blogs

What is dimensionality reduction?Introduced in 2009, single-cell RNA sequencing (scRNA-Seq) allows researchers to observe cellular heterogeneity of the transcriptome at the resolution of individual cells. This method produces vast amounts of data with expression...

t-SNE method- Dimensionality Reduction in Single Cell Genomics

by Xuan Nguyen | Mar 8, 2022 | All Blogs, Bioinformatics & single cell data analysis blogs

Dimension reduction methods – t-SNEIn the previous blog, we have introduced dimension reduction in single-cell RNA-Sequencing (scRNA-Seq) and PCA as one dimension reduction method. We have learned that single cell data are sparse, noisy, and high-dimensional and...

PCA method – Dimensionality Reduction in Single Cell Genomics

by Xuan Nguyen | Mar 8, 2022 | All Blogs, Bioinformatics & single cell data analysis blogs

Dimensional reduction methods – PCAIn the previous blog, we introduced dimension reduction in single cell RNA-Sequencing (scRNA-Seq). We have learned that single cell data are sparse, noisy, and high-dimensional and that dimension reduction is needed to turn the...

Pre-processing of single cell data – A comparison of dropSeqPipe and Kallisto-bustools

by Xuan Nguyen | Jan 25, 2022 | All Blogs, Bioinformatics & single cell data analysis blogs

There is a wealth of analysis options for single cell data out there, which can be daunting for new users. We will discuss two popular pipelines that are tailored to biologists with some computational knowledge. This entails pre-processing through command line on...

From Seurat object to UMAP – An R tutorial

by Juliane Fischer | May 11, 2021 | All Blogs, Bioinformatics & single cell data analysis blogs

Visualizing single cell data using Seurat – a beginner’s guideIn the single cell field, large amounts of data are produced but bioinformaticians are scarce. Therefore, it is an important (and much sought-after) skill for biologists who are able take data into...