Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ggjlab/scHCL
https://github.com/ggjlab/scHCL
Last synced: 3 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/ggjlab/scHCL
- Owner: ggjlab
- Created: 2019-01-26T08:21:28.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-04-18T12:46:30.000Z (about 4 years ago)
- Last Synced: 2023-10-20T19:59:11.850Z (8 months ago)
- Language: R
- Size: 28.7 MB
- Stars: 43
- Watchers: 3
- Forks: 9
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Lists
- awesome-biomedical-machine-learning - scHCL: A tool defines cell types in human based on single-cell digital expression
README
# scHCL
#### A tool defines cell types in human based on single-cell digital expression
At first scHCL is a breif R package for large scale data(large DGE) from scHCL online function [Human Cell Landscape](http://bis.zju.edu.cn/HCL) ,to alleviate burdens of our main Server.
Now we add a UI for visulizing the scHCL reuslt.
### Installation
```R
#This require devtools
install.packages('devtools')
library(devtools)
# scHCL requires ggplot2/reshape2/plotly/shiny/shinythemes/shiny
install_github("ggjlab/scHCL")
```
### Quick Start
```R
library(scHCL)
# hcl_lung is an example expression matrix from HCL project.
> data(hcl_lung)
> dim(hcl_lung)
[1] 2884 80
# 2884 genes expression value of 80 cells
# scHCL has two parameters , single cell expression matrix(scdata) and
# the number of most similar cell types
> hcl_result <- scHCL(scdata = hcl_lung, numbers_plot = 3)
```
The return of scHCL() is a list which contains 4 parts.
* cors_matrix: Pearson correlation coefficient matrix of each cell and cell type.
* top_cors: equals to numbers_plot
* scHCL: the most relevant cell type for each query cell
* scHCL_probility: the top n relevant cell types for each query cell
```R
# open shiny for visualize result for scHCL
scHCL_vis(hcl_result)
```
scHCL_vis() provides a bref function for visualizing and downloading of scHCL results
