Journal
BMC GENOMICS
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s12864-021-07469-6
Keywords
Single cell; RNA-Seq; UMI; Barcode; ddSEQ; 10x; Snakemake; R shiny
Funding
- German Research Foundation [DFG KFO 309 P2/P5/P6/P7/P8/Z01, SFB1021 Z02, SFB-TR84 B/08]
- BMBF [FKZ 031A533]
- Projekt DEAL
Ask authors/readers for more resources
WASP is a software for processing Drop-Seq-based scRNA-Seq data, enabling generation of gene expression matrices, clustering of cellular populations, and interactive graphical visualization. It offers an intuitive interface and modular design for easy handling and exploration of scRNA-seq data by researchers.
Background The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (sub-)cellular populations. Furthermore, scRNA-seq is almost ubiquitously applicable in medical and biological research. However, these new opportunities are accompanied by additional challenges for researchers regarding data analysis, as advanced technical expertise is required in using bioinformatic software. Results Here we present WASP, a software for the processing of Drop-Seq-based scRNA-Seq data. Our software facilitates the initial processing of raw reads generated with the ddSEQ or 10x protocol and generates demultiplexed gene expression matrices including quality metrics. The processing pipeline is realized as a Snakemake workflow, while an R Shiny application is provided for interactive result visualization. WASP supports comprehensive analysis of gene expression matrices, including detection of differentially expressed genes, clustering of cellular populations and interactive graphical visualization of the results. The R Shiny application can be used with gene expression matrices generated by the WASP pipeline, as well as with externally provided data from other sources. Conclusions With WASP we provide an intuitive and easy-to-use tool to process and explore scRNA-seq data. To the best of our knowledge, it is currently the only freely available software package that combines pre- and post-processing of ddSEQ- and 10x-based data. Due to its modular design, it is possible to use any gene expression matrix with WASP's post-processing R Shiny application. To simplify usage, WASP is provided as a Docker container. Alternatively, pre-processing can be accomplished via Conda, and a standalone version for Windows is available for post-processing, requiring only a web browser.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available