Dataset Information
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis.
Ontology highlight
ABSTRACT: Background
Single-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, nonexpert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines.Results
We have developed cellsnake, a comprehensive, reproducible, and accessible single-cell data analysis workflow, to overcome these problems. Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples.Conclusion
As an open-source tool, cellsnake is accessible through Bioconda, PyPi, Docker, and GitHub, making it a cost-effective and user-friendly option for researchers. By using cellsnake, researchers can streamline the analysis of scRNA-seq data and gain insights into the complex biology of single cells.
SUBMITTER: Umu SU
PROVIDER: S-EPMC10603768 | biostudies-literature | 2022 Dec
REPOSITORIES: biostudies-literature
Publications
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis.
GigaScience 20221201
<h4>Background</h4>Single-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, nonexpert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines.<h4>Results</h4>We have developed cellsnake, a comprehen ...[more]
