Several popular tools such as Cell Ranger (10X genomics), Seurat, and Scanpy were developed and used by researchers. Which tool do you recommend most? What are the next questions/tools should be solved/developed for scRNAseq analysis.
Hello
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2599-6
https://www.frontiersin.org/research-topics/9077/bioinformatics-analysis-of-single-cell-sequencing-data-and-applications-in-precision-medicine
My recommendations:
*Open-source command-line packages:
- Hera-T for transcript quantification: https://www.biorxiv.org/content/10.1101/530501v1
- Seurat for visualization and downstream analysis: https://satijalab.org/seurat/
*Software with interactive UI:
- BioTuring Browser: https://blog.bioturing.com/2018/12/05/bioturing-browser-the-software-to-resolve-major-challenges-in-single-cell-rna-seq-data-analysis/
I think the next critical problems to be solved is how to effectively combine multiple single-cell datasets, considering their variations in technologies, methods, etc.
One can use our browser-based software BIOMEX, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX is extremely use friendly and designed for bench scientist of non computational background. BIOMEX is useful for metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others.
https://pubmed.ncbi.nlm.nih.gov/32392297/
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