README.md

In scClassify: scClassify: single-cell Hierarchical Classification

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 [e-mail] or [e-mail].

Reference

scClassify: hierarchical classification of cells

Yingxin Lin, Yue Cao, Hani J Kim, Agus Salim, Terence P. Speed, Dave Lin, Pengyi Yang, Jean Yee Hwa Yang

bioRxiv 776948; doi: https://doi.org/10.1101/776948

scClassify documentation built on Nov. 8, 2020, 8:08 p.m.