ProjectSVR/README.Rmd at main · JarningGau/ProjectSVR · GitHub

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---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


```{r echo=FALSE, results="hide", message=FALSE}
library("badger")
```

# ProjectSVR <img src="man/figures/ProjectSVR-logo.png" align="right" width=80px/>

`r badge_devel("JarningGau/ProjectSVR", "green")`

`ProjectSVR` is a machine learning-based algorithm for mapping the query cells onto well-constructed reference atlas.

<img src="man/figures/ProjectSVR-workflow.png" width="600" />


## Citation
Jianing Gao, et al., ProjectSVR: mapping single-cell RNA-seq data to reference atlases by supported vector regression, Briefings in Bioinformatics, Volume 26, Issue 6, November 2025, bbaf586, https://doi.org/10.1093/bib/bbaf586

## Related resources

### Quick start dataset

The data of [quick start](https://jarninggau.github.io/ProjectSVR/articles/quick_start.html) for ProjectSVR is available at https://zenodo.org/record/8147304 or 百度云盘(https://pan.baidu.com/s/13qSpcaldyQ9MUVCIaYSUIQ) 提取码: psvr

### Reference atlas

The reference cell atlases involved in ProjectSVR paper are available at https://zenodo.org/record/8350746 or 百度云盘(https://pan.baidu.com/s/1fNG5PcgqWiPZi3erkewA5w) 提取码: psvr

### Query dataset

The query datasets involved in ProjectSVR paper are available at https://zenodo.org/record/8350748 or 百度云盘(https://pan.baidu.com/s/1yGdhcwBIxodinRpppPHkQw) 提取码: psvr

### Pre-built reference model

You can download pre-build reference models from [Zenodo](https://zenodo.org/record/8350732) or 百度云盘(https://pan.baidu.com/s/1yBWifQHimRNun1jgcYVEPg) 提取码: psvr

| Name                                                         | Source                                       | Version | Download                                                     |
| ------------------------------------------------------------ | -------------------------------------------- | ------- | ------------------------------------------------------------ |
| PBMC (DISCO)                                                 | https://www.immunesinglecell.org/atlas/blood | 0.2     | [download](https://zenodo.org/record/8350732/files/model.disco_pbmc.rds) |
| Mouse testicular cell atlas (mTCA)                           | This paper                                   | 0.2     | [download](https://zenodo.org/record/8350732/files/model.mTCA.rds) |
| Maternal-fetal interface atlas (Vento 2018)                  | https://doi.org/10.1038/s41586-018-0698-6    | 0.2     | [download](https://zenodo.org/record/8350732/files/model.Vento2018.MFI.rds) |
| Pan cancer tumor infiltrated CD4+ T cell landscape (Zheng 2021) | https://doi.org/10.1126/science.abe6474      | 0.2     | [download](https://zenodo.org/record/8350732/files/model.Zheng2021.CD4Tcell.rds) |
| Pan cancer tumor infiltrated CD8+ T cell landscape (Zheng 2021) | https://doi.org/10.1126/science.abe6474      | 0.2     | [download](https://zenodo.org/record/8350732/files/model.Zheng2021.CD8Tcell.rds) |


## Tutorials

The ProjectSVR webpage with all the documentation and tutorials is [here](https://jarninggau.github.io/ProjectSVR/).

We have various examples, including:

A generic quick start tutorial on a demo PBMC scRNA-seq dataset.

- [Quick start: mapping PBMC dataset onto pre-build PBMC reference.](https://jarninggau.github.io/ProjectSVR/articles/quick_start.html)

Tutorials on how to build projection models for reference atlas.

- [DISCO blood atlas](https://jarninggau.github.io/ProjectSVR/articles/model_pbmc.html)

- [Maternal-fetal interface atlas](https://jarninggau.github.io/ProjectSVR/articles/model_mfia.html)

- [Pan-cancer T cell lanscape](https://jarninggau.github.io/ProjectSVR/articles/model_pctl.html)

- [Mouse testicular cell atlas](https://jarninggau.github.io/ProjectSVR/articles/model_mtca.html)

Tutorials on how to project the query datasets onto reference atlas via pre-build models.

- [Decidual immune microenvironment of RPL patients](https://jarninggau.github.io/ProjectSVR/articles/mapQuery_immune_RPL.html)

- [ICB responsiveness of BRCA](https://jarninggau.github.io/ProjectSVR/articles/mapQuery_ICB_BRCA.html)

- [Genetic perturbed germ cells (Zfp541-KO)](https://jarninggau.github.io/ProjectSVR/articles/mapQuery_Zfp541-KO.html)

- [Genetic perturbed germ cells (Ythdc2-KO)](https://jarninggau.github.io/ProjectSVR/articles/mapQuery_Ythdc2-KO.html)

- [In vitro induced meiosis](https://jarninggau.github.io/ProjectSVR/articles/mapQuery_invitro_meiosis.html)

A tutorial on how to train a model to predict pseudotime.

- [Training the reference pseudotime model](https://jarninggau.github.io/ProjectSVR/articles/misc_Ythdc2-KO_pseudotime.html)

A tutorial on how to train a multi-classifier for cell type auto annotation.

- [Training an ensemble SVM model for cell type prediction](https://jarninggau.github.io/ProjectSVR/articles/misc_disco_pbmc_svm.html)

## Installation

Install the development version from GitHub use:

```{r eval=FALSE}
install.packages("devtools")
devtools::install_github("JarningGau/ProjectSVR")
```

`ProjectSVR` has been successfully installed and test on ubuntu, centOS and wsl2.

### Dependencies

- R >= 4.1

### External packages

Install `AUCell` or `UCell` for signature score calculation.

```{r eval=FALSE}
## install UCell
# R = 4.3
BiocManager::install("UCell") # or
# R < 4.3
remotes::install_github("carmonalab/UCell", ref="v1.3")
## install AUCell
BiocManager::install("AUCell")
```

We provided a wrapper [`RunCNMF`](https://jarninggau.github.io/ProjectSVR/reference/RunCNMF.html) of python pacakge [`cnmf`](https://github.com/dylkot/cNMF) for feature selection. If you want to use it, you should install `cnmf` through `reticulate`.

```{r eval=FALSE}
install.packages("reticulate")
reticulate::install_miniconda()
## install sceasy for single cell data format transformation.
devtools::install_github("cellgeni/sceasy")
reticulate::py_install("anndata")
## install cnmf package via reticulate
reticulate::py_install("cnmf")
```

## Benchmark results

Benchmark results of ProjectSVR and other reference mapping algorithms were listed at https://github.com/JarningGau/ProjectSVR-benchmark/

## Code of Conduct

  Please note that the ProjectSVR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.