MCView

MCView creates a shiny-app facilitating interactive exploration and annotation of metacell models. Metacell itself is described here. You can also explore examples of MCV output for PBMC and Mouse organogenesis on the Tanay group server.

Installation

Install the latest github release:

remotes::install_github("tanaylab/MCView", ref = remotes::github_release())

Or install the development version:

remotes::install_github("tanaylab/MCView")

Usage

See the vignette.

Tl;dr:

Initialize a new project:

MCView::create_project("PBMC")

Import a dataset:

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 script.

Run the app:

You can run the app from R using:

MCView::run_app("PBMC", launch.browser = TRUE)

Or from shell:

Rscript start_app.R PBMC