scMiko

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scMiko

scMiko is an R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

Documentation and tutorials can be found at https://nmikolajewicz.github.io/scMiko/. To get started, refer to our getting started with scMiko article.

scMiko is hosted on Github, and the source code can be cloned at https://github.com/NMikolajewicz/scMiko.

scMiko is developed and tested in Windows, however it is expected to work in MacOS X and Linux.

scPipeline

The scPipeline analysis pipeline is a modular collection of R markdown scripts that have been developed in tandem with the scMiko package. The scPipeline pipeline generates dashboard reports for scRNAseq analyses.

Documentation and tutorials for scPipeline workflows can also be found at https://nmikolajewicz.github.io/scMiko/. To get started, see our getting started with scPipeline article.

scPipeline source code can be accessed at https://github.com/NMikolajewicz/scPipeline.

Citation

if using scPipeline or scMiko, please consider citing our work: Mikolajewicz, N., Gacesa, R., Aguilera-Uribe, M., Brown, K. R., Moffat, J., & Han, H. (2022). Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline. Communications Biology, 5(1), 1-14.