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scClassify: hierarchical classification of cells

Single cell classification via cell-type hierarchies based on ensemble learning and sample size estimation.

Installation

Install Bioconductor packages S4Vectors, hopach and limma packages using BiocManager:

# install.packages("BiocManager")
BiocManager::install(c("S4Vectors", "hopach", "limma"))

Then install the latest scClassify using devtools (For R >= 4.0):

library(devtools)
devtools::install_github("SydneyBioX/scClassify")

For R >= 3.6, install scClassify(v0.2.3) via

devtools::install_github("SydneyBioX/scClassify@085c72f")

Vignette and Shiny app

You can find the vignette at this website (https://sydneybiox.github.io/scClassify/index.html):

Also, you can find our interactive shiny application (beta) at this website: http://shiny.maths.usyd.edu.au/scClassify.

Pretrained models

Currently available pre-trained scClassify models (in scClassifyTrainModel class)

Tissue Organism Training Data Accession Summary Download .rds Gene Name Format
Primary visual cortex mouse Tasic (2018) GSE115746 link link Mm Gene Symbol
Primary visual cortex mouse Tasic (2016) GSE71585 link link Mm Gene Symbol
Visual cortex mouse Hrvatin GSE102827 link link Mm Gene Symbol
Lung mouse Cohen GSE119228 link link Mm Gene Symbol
Kidney mouse Park GSE107585 link link Mm Gene Symbol
Liver human MacParland GSE115469 link link Hs Gene Symbol
Liver human Aizarani GSE124395 link link Hs Gene Symbol
Pancreas human Xin GSE81608 link link Hs Gene Symbol
Pancreas human Wang GSE83139 link link Hs Gene Symbol
Pancreas human Lawlor GSE86469 link link Hs Gene Symbol
Pancreas human Segerstolpe E-MTAB-5061 link link Hs Gene Symbol
Pancreas human Muraro GSE85241 link link Hs Gene Symbol
Pancreas human Baron GSE84133 link link Hs Gene Symbol
Pancreas human joint - link link Hs Gene Symbol
Melanoma human Li GSE123139 link link Hs Gene Symbol
PBMC human Ding (joint) - link link Mm EMSEMBL ID
Tabula Muris mouse Tabula Muris GSE109774 link link Mm Gene Symbol

Contact us

If you have any enquiries, especially about performing scClassify to classify your cells or to build your own models, please contact yingxin.lin@sydney.edu.au or bioinformatics@maths.usyd.edu.au.

Reference

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

Yingxin Lin, Yue Cao, Hani Kim, Agus Salim, Terence Speed, David Lin, Pengyi Yang† & Jean Yang†. Molecular Systems Biology, 2020, 16, e9389. Full Text; BioC R package

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Hierarchical classification of cells

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