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Tag Archives: scRNA-seq

The Basics of DESeq2 – A Powerful Tool in Differential Expression Analysis for Single-cell RNA-Seq
deseq2 single cell example

Differential expression analysis is a common step in a Single-cell RNA-Seq data analysis workflow. In our previous post, we have given an overview of differential expression analysis tools in single-cell RNA-Seq. This time, we’d like to discuss a frequently used tool – DESeq2 (Love, Huber, & Anders, 2014).  According to […]

BioTuring Data Science Platform: A Jupyter notebook library of latest methods for single-cell analysis in R and Python
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Did you know that by the end of 2021, the number of tools for single-cell RNA-sequencing (scRNA-seq) data analysis has passed 1,000? (Zappia and Theis, 2021) This massive resource accelerates the exploration of single-cell data. At the same time, the plethora of options poses several challenges for researchers, such as:   […]

The Maze of Differential Gene Expression Analysis in Single-cell RNA-Seq
scrna seq differential expression - venice

Single-cell RNA sequencing (scRNA-seq) unfolds biological processes at individual cell resolution. One key step that makes up the power of scRNA-seq is the spotting of differentially expressed (DE) genes. However, characteristics like high heterogeneity and data sparsity (high zero counts) are the main obstacles in finding DE genes in scRNA-seq […]

Batch Effect in Single-Cell RNA-Seq: Frequently Asked Questions and Answers
batch effect single cell rna seq 2

One essential step in the preprocessing of single-cell RNA-Seq data (scRNA-seq) is batch effect correction. However, much confusion remained around this step. In this article, let’s address the most frequently asked questions about handling batch effect in single-cell RNA-Seq. .  What is Batch Effect in Single-cell RNA-Seq? Batch effect happens […]

scRNA-Seq Cell Type Annotation: Common Approaches and Tools
scrna seq cell type annotation talk2data

Assigning cell type identity to cells is a basic yet vital step required in single-cell RNA Sequencing data analysis (scRNA-Seq), often done after dimensionality reduction and scRNA-Seq clustering . If you have successfully captured informative clusters, it’s time to face an even harder challenge: identify what cell type or cell […]

How to explore “Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution” (Duclos et. al 2019) | BioTuring Cellpedia

Multiple studies have shown smoking’s effects on the human bronchi. However, few have characterized its precise impact at cellular resolution. Published recently on Science Advances, a study by Duclos and colleagues has employed single-cell RNA sequencing into exploring the cellular changes in the human bronchial epithelium between current and never […]