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):

• scClassify Model Building and Prediction: https://sydneybiox.github.io/scClassify/articles/scClassify.html
• Sample size calculation: https://sydneybiox.github.io/scClassify/articles/webOnly/sampleSizeCal.html
• Performing scClassify using pretrained models: https://sydneybiox.github.io/scClassify/articles/pretrainedModel.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