<!-- README.md is generated from README.Rmd. Please edit that file --> # Chevreul This package includes a set of Shiny apps for exploring single cell RNA datasets processed as a SingleCellExperiment A demo using a human gene transcript dataset from Shayler et al. (link) is available <a href="http://cobrinik-1.saban-chla.usc.edu:8080/app/objectApp" target="_blank" rel="noopener noreferrer">here</a> There are also convenient functions for: - Clustering and Dimensional Reduction of Raw Sequencing Data. - Integration and Label Transfer - Louvain Clustering at a Range of Resolutions - Cell cycle state regression and labeling > \[!WARNING\] chevreulPlot was designed for full-length smart-seq based > single cell data. Default settings may not be appropriate for droplet > (10x) data, though most can be adjusted. Keep in mind best practices > regarding normalization, dimensional reduction, etc. when using. ## Installation You can install the released version of chevreulPlot from <a href="https://github.com/whtns/chevreul" target="_blank" rel="noopener noreferrer">github</a> with: ### Install locally and run in three steps: You can install chevreulPlot locally using the following steps: ``` r install.packages("devtools") devtools::install_github("whtns/chevreul") chevreul::create_project_db() ``` You can also customize the location of the app using these steps: ``` r devtools::install_github("whtns/chevreul") chevreul::create_project_db(destdir = "/your/path/to/app") ``` ## TLDR chevreulPlot provides a single command to: - construct a SingleCellExperiment object. - filter genes by minimum expression and ubiquity - normalize and scale expression by any of several methods packaged in SingleCellExperiment ## Run clustering on a single object By default clustering will be run at ten different resolutions between 0.2 and 2.0. Any resolution can be specified by providing the resolution argument as a numeric vector. ``` r clustered_sce <- clustering_workflow(chevreul_sce, experiment_name = "sce_hu_trans", organism = "human" ) ``` ## Get a first look at a processed dataset using an interactive shiny app ``` r minimalChevreulApp(chevreul_sce) ```