We present a novel method called muLtimodal co-Expressed GEnes finDer (LEGEND) that performs integrated gene clustering on scRNA-seq and SRT data to identify co-expressed genes at both the cell type and tissue domain levels. LEGEND performs a hierarchical gene clustering with the aim of maximizing intra-cluster redundancy and inter-cluster complementarity.
GeneClust is a computational feature selection method for scRNA-seq cell clustering. GeneClust groups genes into clusters from which genes are evaluated and selected with the aim of maximizing relevance, minimizing redundancy and preserving complementarity.
popuDE is an R package for the statistical modeling of the gene differential expression (DE) in scRNA-seq data. It identifies cell-type specific genes (markers) that consistently appear in historical population-level scRNA-seq (scRNA-seq) data. popuDE is built on top of the R package SingleCellExperiment and supports parallel computation. Except from our proposed method, popuDE also provides a common interface for classic DE methods such as the Wilcoxon test, t-test and DESeq2.
I am the maintainer of this package. The core function,
popuDE(), was written by Luxiao Chen. I wrote other functions and built the package.
ZUEL-thesis is a $\LaTeX$ template for the bachelor thesis of ZUEL. I created this template when I was writing my undergraduate thesis.