# scClassify: hierarchical classification of cells
<img src="man/figures/scClassifySticker.png" align="right" width="200"/>
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`:
```r
# install.packages("BiocManager")
BiocManager::install(c("S4Vectors", "hopach", "limma"))
```
Then install the latest `scClassify` using `devtools` (For R >= 4.0):
```r
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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115746) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Tasic2018_mouseNeuronal.html)| [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainTasicV2resClass.rds) | Mm Gene Symbol|
| Primary visual cortex | mouse | Tasic (2016) | [GSE71585](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Tasic2016_mouseNeuronal.html)| [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainTasicV1resClass.rds) | Mm Gene Symbol|
| Visual cortex | mouse | Hrvatin | [GSE102827](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102827) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Hrvatin_mouseNeuronal.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainHrvatinresClass.rds) | Mm Gene Symbol|
| Lung | mouse | Cohen | [GSE119228](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119228) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Cohen_mouseLung.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainCohenresClass.rds) | Mm Gene Symbol|
| Kidney | mouse | Park | [GSE107585](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107585) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Park_mouseKidney.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainParkresClass.rds) | Mm Gene Symbol|
| Liver | human | MacParland | [GSE115469](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115469) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/MacParlandres_humanLiver.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainMacParlandresClass.rds) | Hs Gene Symbol|
| Liver | human | Aizarani | [GSE124395](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124395) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Aizarani_humanLiver.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainAizaraniresClass.rds) | Hs Gene Symbol|
| Pancreas | human | Xin | [GSE81608](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81608) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Xin_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainXinClass.rds) | Hs Gene Symbol|
| Pancreas | human | Wang | [GSE83139](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83139) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Wang_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainWangClass.rds) | Hs Gene Symbol|
| Pancreas | human | Lawlor | [GSE86469](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86469) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Lawlor_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainLawlorClass.rds) | Hs Gene Symbol|
| Pancreas | human | Segerstolpe | [E-MTAB-5061](https://www.ebi.ac.uk/arrayexpress/E-MTAB-5061) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Segerstolpe_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainSegerstolpeClass.rds) | Hs Gene Symbol|
| Pancreas | human | Muraro | [GSE85241](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85241) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Muraro_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainMuraroClass.rds) | Hs Gene Symbol|
| Pancreas | human | Baron | [GSE84133](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84133) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Baron_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainBaronClass.rds) | Hs Gene Symbol|
| Pancreas | human | joint | - | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Joint_humanPancreas.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/jointPancreasClass.rds) | Hs Gene Symbol|
| Melanoma | human | Li | [GSE123139](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123139) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Li_humanMelanoma.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainLiresClass.rds) | Hs Gene Symbol|
| PBMC | human | Ding (joint) | - | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/Joint_humanPBMC.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/jointPBMCClass.rds) | Mm EMSEMBL ID|
| Tabula Muris | mouse | Tabula Muris | [GSE109774](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109774) | [link](https://SydneyBioX.github.io/scClassify/articles/webOnly/TabulaMuris.html) | [link](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scClassify/trainTMresClass.rds) | 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](https://doi.org/10.15252/msb.20199389); [BioC R package](http://www.bioconductor.org/packages/release/bioc/html/scClassify.html)
