Artifacts using SingleCellExperiment version 1.2.0-b5

A collection of tools for cancer single cell RNA-seq analysis. Cell clustering and feature gene selection analysis employ maximum likelihood and Bayesian non-negative matrix factorization algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks, quality measures (maximum likelihood) or evidence (Bayesian) with respect to rank. The package includes utilities for downstream analyses, including meta-gene ...

DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results ...