A general view of Python-based scRNA-seq data analysis

Standard procedure of analyzing scRNA dataPre-processing (10x; cellranger)Collect data from 10x. Then use cellranger, a commercial software for data pre-processing, to get cell count matrix.Quality control (filter; doublets)After getting count matrix, quality control (QC) is needed to be implemented first. The purpose of QC has two sides. Firstly, we have to remove data of low quality, which may reflect the results of analysis. Then, we can examine the distribution of the collected data. In the

Bioinformatics·Science research · 2023-08-24

Single-cell RNA-sequencing

BackgroundDeep sequencing of DNA and RNA from a single cell is of great importance in the investigation of cellular functions. Generally, typical next-generation sequencing experiments often contain the following steps: isolation of single-cell, nucleic acid extraction and amplification, sequencing library preparation, sequencing, and bioinformatic data analysis. However, it is obviously more challenging to perform single-cell sequencing than sequencing from cells in bulk. As the development of

Bioinformatics·Science research · 2023-08-22