ncchung/SeuratAddon: Unsupervised evaluation of cell identities in Seurat

Evaluate cell identities estimated from clustering of scRNA-seq data in the Seurat pipeline. This package provides new functionalities that can be used with a Seurat object. K-means clustering is enhanced with the Kmeans++ initialization for faster convergence and the mini-batch algorithm that can easily scale to millions of single cells. Cell identities that are determined by clustering algorithms are evaluated by the jackstraw methods, providing p-values and posterior inclusion probabilities (PIPs) for individual single cells. These probabilities can be used for feature selection and visualization. In particular, t-SNE projection is improved by hard- or soft-thresholding with PIPs or adjusted p-values.

Getting started

Package details

AuthorNeo Christopher Chung <[email protected]>
MaintainerNeo Christopher Chung <[email protected]>
LicenseGPL-3
Version0.1.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("ncchung/SeuratAddon")
ncchung/SeuratAddon documentation built on Jan. 4, 2019, 12:35 a.m.