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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# MCView
<!-- badges: start -->
<!-- badges: end -->
MCView creates a shiny-app facilitating interactive exploration and annotation of metacell models. Metacell itself is described [here](https://pypi.org/project/metacells/). You can also explore an example of MCV output for [Mouse organogenesis](https://apps.tanaylab.com/MCV/mm_gastru/) on the Tanay group server.
## Installation
Install the latest github release:
```r
remotes::install_github("tanaylab/MCView", ref = remotes::github_release())
```
Or install the development version:
```r
remotes::install_github("tanaylab/MCView")
```
## Usage
See the [vignette](https://tanaylab.github.io/MCView/articles/MCView.html).
Tl;dr:
#### Initialize a new project:
```r
MCView::create_project("PBMC")
```
#### Import a dataset:
```r
MCView::import_dataset(project = "PBMC",
dataset = "PBMC163k",
anndata_file = "raw/metacells.h5ad")
```
> Note: since version 0.2.7, MCView only supports files that were generated by the new metacells version (>= 0.9). If you have an old file, you can convert it using [this](https://github.com/tanaylab/metacells/blob/master/bin/convert_0.8_to_0.9.py) script.
#### Run the app:
You can run the app from R using:
```r
MCView::run_app("PBMC", launch.browser = TRUE)
```
Or from shell:
```bash
Rscript start_app.R PBMC
```