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index.Rmd
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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
This is the website for demonstrating how to use the [`scclusteval`](https://github.com/crazyhottommy/scclusteval) R package. This R package
works with the output from the [Snakemake workflow](https://github.com/crazyhottommy/pyflow_seuratv3_parameter)
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](https://github.com/crazyhottommy/pyflow_seuratv3_parameter) for a neuron dataset
from Allen Brain Institute and you can find the data in the [osf.io](https://osf.io/rfbcg/) link above.
* The 5k pbmc scRNAseq dataset was downloaded from 10x website and made into a `Seruat` object.
* The rds file for the 5- cancer cell line mixology dataset is dowloaded from https://github.com/LuyiTian/sc_mixology
* The 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](https://github.com/satijalab/Integration2019/blob/master/preprocessing_scripts/allen_brain.R). Alternatively, you can download the pre-processed Seurat object [here](https://www.dropbox.com/s/kqsy9tvsklbu7c4/allen_brain.rds?dl=0).
Readers can follow the examples of the mixology and pbmc dataset and explore the
neuron dataset yourself. Have fun!