--- a
+++ b/man/getDiffExp.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/differentialexpression.R
+\name{getDiffExp}
+\alias{getDiffExp}
+\title{getDiffExp}
+\usage{
+getDiffExp(
+  object,
+  assay = NULL,
+  group.by,
+  group.base = NULL,
+  covariates = NULL,
+  method = "DESeq2"
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+if NULL, the default assay will be used, see \link{vrMainAssay}.}
+
+\item{group.by}{the categorical variable from metadata to get differentially expressed features across}
+
+\item{group.base}{Optional, the base category in \code{group.by} which is used as control group}
+
+\item{covariates}{the covariate variable for the design formula}
+
+\item{method}{the method for DE analysis, e.g. DESeq2}
+}
+\description{
+Get differential expression with DESeq2
+}