README.md

In HCBravoLab/TreeSE: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

scTreeViz

This package provides methods to interactively explore and visualize datasets with hierarchies. eg. single cells datasets with hierarchy over cells at different resolutions.

For a walk through of various features of the app, checkout the vignette at

https://hcbravolab.github.io/scTreeViz/Explore-PBMC.html

Installation and requirements

scTreeViz currently requires a development version of epivizrData which supports Sparse Measurements. We plan to push this to bioc soon.

To install scTreeViz,

BiocManager::install("epiviz/epivizrData")
BiocManager::install("HCBravoLab/scTreeViz")

Note: you can also use devtools to install the package from github

Usage

To try out and explore the various features of the package, we provide the PBMC 3K dataset and the vignette Explore-PBMC walks you through the process.

To checkout all the vignettes

library(scTreeViz)
browseVignettes("scTreeViz")

HCBravoLab/TreeSE documentation built on Sept. 27, 2021, 4:19 p.m.