Last updated: 2020-03-23
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Knit directory: EvaluateSingleCellClustering/
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This is the website for demonstrating how to use the scclusteval R package. This R package works with the output from the Snakemake workflow
Readers can download the datasets at https://osf.io/rfbcg/ and follow the analysis in the Rmarkdown files.
You can find the analysis for the mixology dataset and the 5k pbmc dataset in the Content drop list. We also run the Snakemake workflow for a neuron dataset from Allen Brain Institute and you can find the data in the osf.io link above.
The 5k pbmc scRNAseq dataset was downloaded from 10x website and made into a Seruat object.
The Seurat rds file for the 5- cancer cell line mixology dataset is dowloaded from https://github.com/LuyiTian/sc_mixology
The Seurat rds file for the neuron dataset is downloaded from https://satijalab.org/signac/articles/mouse_brain_vignette.html
You can download the raw data for this experiment from the Allen Institute website, and view the code used to construct this object on GitHub. Alternatively, you can download the pre-processed Seurat object here.
Readers can follow the examples of the mixology and pbmc dataset and explore the neuron dataset yourself. Have fun!