diff --git a/DESCRIPTION b/DESCRIPTION
index 29a9b77..d478961 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: Provides data structures and utility functions for gene expression
     probeset summarization and filtering, and interfaces to limma-based
     differential gene expression workflows. The package works with Biobase
     ExpressionSet objects and integrates with the limma framework.
-Depends: R (>= 4.4.0)
+Depends: R (>= 4.1.2)
 Imports:
     methods,
     stats,
diff --git a/man/DesignContrast-class.Rd b/man/DesignContrast-class.Rd
index 62dea53..e56ebf0 100644
--- a/man/DesignContrast-class.Rd
+++ b/man/DesignContrast-class.Rd
@@ -16,9 +16,9 @@ The DesignContrast class represents key information in a designed experiment
 }
 \section{Functions}{
 \itemize{
-\item \code{show(DesignContrast)}: The show method
-
+\item \code{show,DesignContrast-method}: The show method
 }}
+
 \section{Slots}{
 
 \describe{
diff --git a/man/contrastAnnotation.Rd b/man/contrastAnnotation.Rd
index 74cf994..a9b12bb 100644
--- a/man/contrastAnnotation.Rd
+++ b/man/contrastAnnotation.Rd
@@ -25,10 +25,10 @@ Extract the contrast annotation data.frame from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{contrastAnnotation(DesignContrast)}: Return the contrast annotation data.frame
+\item \code{DesignContrast}: Return the contrast annotation data.frame
 from a DesignContrast object
 
-\item \code{contrastAnnotation(DesignContrast) <- value}: Assign a contrast annotation data.frame
+\item \code{DesignContrast}: Assign a contrast annotation data.frame
 to a \code{contrastContrast} object
-
 }}
+
diff --git a/man/contrastMatrix.Rd b/man/contrastMatrix.Rd
index 71f9246..7872728 100644
--- a/man/contrastMatrix.Rd
+++ b/man/contrastMatrix.Rd
@@ -28,12 +28,12 @@ Extract the contrast matrix from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{contrastMatrix(DesignContrast)}: Return the contrast matrix from a DesignContrast
+\item \code{DesignContrast}: Return the contrast matrix from a DesignContrast
 object
 
-\item \code{contrastMatrix(DesignContrast) <- value}: Assign a contrast matrix to a \code{contrastContrast}
+\item \code{DesignContrast}: Assign a contrast matrix to a \code{contrastContrast}
 object
 
-\item \code{contrastMatrix(MArrayLM)}: Extract contrast matrix from an object of MArrayLM
-
+\item \code{MArrayLM}: Extract contrast matrix from an object of MArrayLM
 }}
+
diff --git a/man/contrastNames.Rd b/man/contrastNames.Rd
index 98e2cf8..8771138 100644
--- a/man/contrastNames.Rd
+++ b/man/contrastNames.Rd
@@ -23,9 +23,9 @@ Extract contrastNames from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{contrastNames(DesignContrast)}: Return contrast names, i.e., column names of the
+\item \code{DesignContrast}: Return contrast names, i.e., column names of the
 contrast matrix
 
-\item \code{contrastNames(MArrayLM)}: Extract contrast names from an object of MArrayLM
-
+\item \code{MArrayLM}: Extract contrast names from an object of MArrayLM
 }}
+
diff --git a/man/contrastSampleIndices.Rd b/man/contrastSampleIndices.Rd
index da232d8..dc2d5bf 100644
--- a/man/contrastSampleIndices.Rd
+++ b/man/contrastSampleIndices.Rd
@@ -25,11 +25,11 @@ Return indices of samples involved in the given contrast of two or more coeffici
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{contrastSampleIndices(object = DesignContrast, contrast = character)}: Use character string to specify the contrast
-
-\item \code{contrastSampleIndices(object = DesignContrast, contrast = numeric)}: Use integer indices to specify the contrast
+\item \code{object = DesignContrast,contrast = character}: Use character string to specify the contrast
 
+\item \code{object = DesignContrast,contrast = numeric}: Use integer indices to specify the contrast
 }}
+
 \examples{
 ## one-way ANOVA
 myDesCon <- parseDesignContrast(sampleGroups="As,Be,As,Be,As,Be",
diff --git a/man/designMatrix.Rd b/man/designMatrix.Rd
index c17c6fa..d666b77 100644
--- a/man/designMatrix.Rd
+++ b/man/designMatrix.Rd
@@ -28,12 +28,12 @@ Extract the design matrix from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{designMatrix(DesignContrast)}: Return the design matrix from a DesignContrast
+\item \code{DesignContrast}: Return the design matrix from a DesignContrast
 object
 
-\item \code{designMatrix(DesignContrast) <- value}: Assign a design matrix to a \code{DesignContrast}
+\item \code{DesignContrast}: Assign a design matrix to a \code{DesignContrast}
 object
 
-\item \code{designMatrix(MArrayLM)}: Extract design matrix from an object of MArrayLM
-
+\item \code{MArrayLM}: Extract design matrix from an object of MArrayLM
 }}
+
diff --git a/man/designVariables.Rd b/man/designVariables.Rd
index 664bf55..21fbb88 100644
--- a/man/designVariables.Rd
+++ b/man/designVariables.Rd
@@ -20,7 +20,7 @@ Extract design variable names from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{designVariables(DesignContrast)}: Return the names of variables (column names) 
+\item \code{DesignContrast}: Return the names of variables (column names) 
 in the design matrix of a DesignContrast object
-
 }}
+
diff --git a/man/dispGroups.Rd b/man/dispGroups.Rd
index e4c1d81..30b68d9 100644
--- a/man/dispGroups.Rd
+++ b/man/dispGroups.Rd
@@ -20,7 +20,7 @@ Extract displayed group labels from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{dispGroups(DesignContrast)}: Return the sample groups from a DesignContrast object
+\item \code{DesignContrast}: Return the sample groups from a DesignContrast object
 , using display labels
-
 }}
+
diff --git a/man/exprsToLong.Rd b/man/exprsToLong.Rd
index 7cde419..293696b 100644
--- a/man/exprsToLong.Rd
+++ b/man/exprsToLong.Rd
@@ -44,8 +44,8 @@ Transform an expression matrix to long table
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{exprsToLong(matrix)}: The method for matrix as input
-
-\item \code{exprsToLong(eSet)}: The method for eSet as input
+\item \code{matrix}: The method for matrix as input
 
+\item \code{eSet}: The method for eSet as input
 }}
+
diff --git a/man/formatGmt.Rd b/man/formatGmt.Rd
index a395da0..a84b582 100644
--- a/man/formatGmt.Rd
+++ b/man/formatGmt.Rd
@@ -40,17 +40,17 @@ Resulting string(s) can be exported into \code{GMT} file by
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{formatGmt(title = character, comment = character, genes = character)}: title, comment, and genes are one character string
+\item \code{title = character,comment = character,genes = character}: title, comment, and genes are one character string
 
-\item \code{formatGmt(title = character, comment = missing, genes = character)}: title and genes are both one character string, comments are missing
+\item \code{title = character,comment = missing,genes = character}: title and genes are both one character string, comments are missing
 
-\item \code{formatGmt(title = character, comment = character, genes = list)}: title and comments are both vectors of character
+\item \code{title = character,comment = character,genes = list}: title and comments are both vectors of character
 strings, genes are a list of the same length
 
-\item \code{formatGmt(title = character, comment = missing, genes = list)}: title is vectors of character strings, comments are
+\item \code{title = character,comment = missing,genes = list}: title is vectors of character strings, comments are
 missing, genes are a list of the same length as the title
-
 }}
+
 \examples{
 
 formatGmt(title="GeneSet0", comment="My geneset", genes=c("MAPT", "MAPK", "AKT1"))
diff --git a/man/groups.Rd b/man/groups.Rd
index 19dcc43..a7dfc57 100644
--- a/man/groups.Rd
+++ b/man/groups.Rd
@@ -20,6 +20,6 @@ Extract sample groups from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{groups(DesignContrast)}: Return the raw sample groups from a DesignContrast object
-
+\item \code{DesignContrast}: Return the raw sample groups from a DesignContrast object
 }}
+
diff --git a/man/nContrast.Rd b/man/nContrast.Rd
index f9c3271..e3c6f30 100644
--- a/man/nContrast.Rd
+++ b/man/nContrast.Rd
@@ -20,7 +20,7 @@ Extract the number of contrasts from an object
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{nContrast(DesignContrast)}: Return the number of contrasts in a DesignContrast
+\item \code{DesignContrast}: Return the number of contrasts in a DesignContrast
 object
-
 }}
+
diff --git a/man/readGctCls.Rd b/man/readGctCls.Rd
index 4a6592d..f344b42 100644
--- a/man/readGctCls.Rd
+++ b/man/readGctCls.Rd
@@ -60,9 +60,9 @@ See example below.
 }
 \section{Functions}{
 \itemize{
-\item \code{readGct()}: readGct uses the C implementation of reading in a gct file
-
+\item \code{readGct}: readGct uses the C implementation of reading in a gct file
 }}
+
 \note{
 The \code{readGct} function is a wrapper of the
 \link[ribiosIO]{read_gct_matrix} function in the \code{ribiosIO} package,
diff --git a/man/removeAllZeroVar.Rd b/man/removeAllZeroVar.Rd
index 946ccfc..40661d4 100644
--- a/man/removeAllZeroVar.Rd
+++ b/man/removeAllZeroVar.Rd
@@ -37,11 +37,11 @@ Remove all-zero variables from design matrix and the corresponding contrast matr
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{removeAllZeroVar(matrix)}: S3 function for matrix as input
-
-\item \code{removeAllZeroVar(DesignContrast)}: S3 function for matrix as input
+\item \code{matrix}: S3 function for matrix as input
 
+\item \code{DesignContrast}: S3 function for matrix as input
 }}
+
 \examples{
 myTestDesign <- matrix(c(1,1,1,1, 1,1,0,0,0,0,1,1,0,0,0,0), 
   byrow=FALSE, nrow=4L, 
diff --git a/man/writeGct.Rd b/man/writeGct.Rd
index 10d6d36..54a4ef4 100644
--- a/man/writeGct.Rd
+++ b/man/writeGct.Rd
@@ -31,11 +31,11 @@ Export matrix or eSet that can be coerced as one into gct/cls files
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{writeGct(matrix)}: Method for matrix as input, 
+\item \code{matrix}: Method for matrix as input, 
 feta.name and feat.desc are passed to \code{write_gct}.
 
-\item \code{writeGct(eSet)}: Use \code{eSet} as input. \code{feat.name} and \code{feat.desc} are 
+\item \code{eSet}: Use \code{eSet} as input. \code{feat.name} and \code{feat.desc} are 
 variable (column) names in \code{fData}.
-
 }}
+
 \keyword{methods}
diff --git a/man/writeGctCls.Rd b/man/writeGctCls.Rd
index 274b4bc..8958aa6 100644
--- a/man/writeGctCls.Rd
+++ b/man/writeGctCls.Rd
@@ -75,9 +75,9 @@ certain degree generic: it can be a character string or integer index of the
 }
 \section{Functions}{
 \itemize{
-\item \code{writeCls()}: writeCls
-
+\item \code{writeCls}: writeCls
 }}
+
 \examples{
 
 data(sample.ExpressionSet, package="Biobase")