diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..77fae88
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,33 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+      - dev-am
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}
diff --git a/NAMESPACE b/NAMESPACE
index 719652b..d68078d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -52,6 +52,7 @@ export(report_impacted_pathway)
 export(report_integrated_sce)
 export(report_merged_sce)
 export(report_qc_sce)
+export(volcano_plot)
 export(write_celltype_mappings)
 export(write_sce)
 export(write_sparse_matrix)
diff --git a/R/cluster_sce.R b/R/cluster_sce.R
index c1b6347..6436b8e 100644
--- a/R/cluster_sce.R
+++ b/R/cluster_sce.R
@@ -2,9 +2,8 @@
 #' Cluster SingleCellExperiment with monocle3::cluster_cells
 #'
 #' @param sce a SingleCellExperiment object
-#' @param reduction_methods one or more of "PCA", "tSNE", "UMAP", "UMAP3D"
-#' @param pca_dims the number of pca dimensions used
-#' @param ... see uwot::umap for umap options
+#' @param ... see uwot::umap for umap options. Includes reduction_methods one 
+#' or more of "PCA", "tSNE", "UMAP", "UMAP3D"
 #'
 #' @return sce a SingleCellExperiment object annotated with reducedDims
 #'
diff --git a/R/diffexp_models.R b/R/diffexp_models.R
index 1a185c7..23d3bc1 100644
--- a/R/diffexp_models.R
+++ b/R/diffexp_models.R
@@ -664,15 +664,23 @@ perform_de <- function(sce,
 }
 
 
-#' volcano plot
+#' Plot volcano plot for differential expression analysis
 #'
+#' @param dt Differential expression result table from perform_de() function.
+#' @param fc_threshold Fold change threshold for the volcano plot. This will be adjusted and plotted as the log2 fold change.  Default is 1.05.
+#' @param pval_cutoff The adjusted p-value cut-off for the volcano plot. Default is 0.05.
+#' @param n_label The number of top up & down differentially expressed genes to be labeled. Default is 10.
+#' 
+#' @return No return. The plot is printed out.
+#' 
+#' @family differential gene expression
+#' 
 #' @importFrom ggplot2 ggplot geom_point aes coord_cartesian
 #' @importFrom ggrepel geom_text_repel
 #' @importFrom dplyr %>% filter top_n
 #'
-#' @keywords internal
-
-.volcano_plot <- function(dt,
+#' @export
+volcano_plot <- function(dt,
                           fc_threshold = 1.05,
                           pval_cutoff = 0.05,
                           n_label = 10) {
diff --git a/R/find_cells_sce.R b/R/find_cells_sce.R
index 0aac580..f30938a 100644
--- a/R/find_cells_sce.R
+++ b/R/find_cells_sce.R
@@ -8,7 +8,7 @@
 #' @param lower see [DropletUtils::emptyDrops()]
 #' @param retain see [DropletUtils::emptyDrops()].  Use "auto" to calculate
 #' the parameter from the top `expect_cells` cells (cellranger method).
-#' @param alpha minimum FDR for [DropletUtils::emptyDrops()]
+# #' @param alpha minimum FDR for [DropletUtils::emptyDrops()]
 #' @param niters the number of Monte Carlo iterations
 #' @param expect_cells the number of cells expected for auto retain
 #' @param alpha_cutoff The alpha cutoff used for Monte Carlo signficance.
diff --git a/R/integrate_sce.R b/R/integrate_sce.R
index 265ce83..ad06362 100644
--- a/R/integrate_sce.R
+++ b/R/integrate_sce.R
@@ -5,9 +5,9 @@
 #'
 #' @param sce a SingleCellExperiment object or merged sce objects
 #' @param method the integration method to use
-#' @param k Inner dimension of factorization (number of factors).
 #'   Set to k=30 as default.
-#' @param ... Additional arguments
+#' @param ... Additional arguments. Such as k Inner dimension of factorization 
+#' (number of factors).
 #'
 #' @return sce SingleCellExperiment object annotated with reducedDims
 #'
diff --git a/R/liger_preprocess.R b/R/liger_preprocess.R
index f77bf9d..778c393 100644
--- a/R/liger_preprocess.R
+++ b/R/liger_preprocess.R
@@ -4,9 +4,11 @@
 #' Split merged object into multiple sce objects and extract sparse matrices:
 #' @param sce SingleCellExperiment object or merged objects
 #' @param k Inner dimension of factorization (number of factors).
+#' @param unique_id_var the colData variable identifying unique samples. 
+#' Default is "manifest".
 #'
 #' Make a Liger object:
-#' @param take.gene.union Whether to fill out raw.data matrices with union
+#' @param take_gene_union Whether to fill out raw.data matrices with union
 #'   of genes across all datasets (filling in 0 for missing data)
 #'   (requires make.sparse=T) (default FALSE).
 #' @param remove.missing Whether to remove cells not expressing any
@@ -15,7 +17,7 @@
 #'   not expressed in any dataset) (default TRUE).
 #'
 #'  Select informative genes:
-#' @param num.genes Number of genes to find for each dataset.
+#' @param num_genes Number of genes to find for each dataset.
 #'   Set to 3000 as default.
 #' @param combine How to combine variable genes across experiments.
 #'   Either "union" or "intersect".
@@ -26,7 +28,10 @@
 #'  Scale genes by root-mean-square across cells:
 #'
 #' Remove cells/genes with no expression across any genes/cells:
-#' @param use.cols Treat each column as a cell (default TRUE)
+#' @param use_cols Treat each column as a cell (default TRUE)
+#' @param num_cores Number of cores used on user's machine to run function. 
+#' Default fouynd by `future::availableCores()`
+#' @param ... Additional arguments.
 #'
 #' @return liger preprocessed object.
 #'
diff --git a/R/liger_reduce_dims.R b/R/liger_reduce_dims.R
index 7a763f1..654067b 100644
--- a/R/liger_reduce_dims.R
+++ b/R/liger_reduce_dims.R
@@ -19,9 +19,9 @@
 #'   this increments the random seed by 1 for each consecutive restart,
 #'   so future factorizations of the same dataset can be run with
 #'   one rep if necessary. (default 1)
-#' @param H.init Initial values to use for H matrices. (default NULL)
-#' @param W.init Initial values to use for W matrix (default NULL)
-#' @param V.init Initial values to use for V matrices (default NULL)
+#' @param h_init Initial values to use for H matrices. (default NULL)
+#' @param w_init Initial values to use for W matrix (default NULL)
+#' @param v_init Initial values to use for V matrices (default NULL)
 #' @param rand_seed Random seed to allow reproducible results (default 1).
 #' @param print_obj Print objective function values after convergence
 #'   (default FALSE).
@@ -40,6 +40,7 @@
 #'   sparse modalities like methylation data). (default FALSE)
 #' @param resolution Controls the number of communities detected.
 #'   Higher resolution -> more communities. (default 1)
+#' @param ... Additional arguments.
 #'
 #' @return liger object with H, H.norm, W, and V slots sets.
 #'
diff --git a/R/model_celltype_freqs.R b/R/model_celltype_freqs.R
index f58a9d0..2a5851a 100644
--- a/R/model_celltype_freqs.R
+++ b/R/model_celltype_freqs.R
@@ -6,6 +6,8 @@
 #' @param celltype_var the colData variable specifying celltype or subtype
 #' @param dependent_var the name of the colData variable for contrasts
 #' @param ref_class the class of dependent_var used as reference
+#' @param var_order Optional re-ordering of subset_group factor levels. Default 
+#' NULL. 
 #' @param ... Additional arguments
 #'
 #' @return results_l a list of results
diff --git a/R/plot_expr_by_numeric_var.r b/R/plot_expr_by_numeric_var.r
index b2ab4d9..0191830 100644
--- a/R/plot_expr_by_numeric_var.r
+++ b/R/plot_expr_by_numeric_var.r
@@ -9,7 +9,7 @@
 #'
 #'
 #' @param sce a SingleCellExperiment object
-#' @param group_var The colData variable for x-axis groups
+#' @param numeric_var The colData variable for x-axis groups. Default is p_tau
 #' @param subset_var The colData variable to subset on
 #' @param subset_group The specific subset_var group to subset
 #' @param gene The gene of interest
diff --git a/R/report_de.R b/R/report_de.R
index 56a2e8f..b81c0e6 100644
--- a/R/report_de.R
+++ b/R/report_de.R
@@ -27,7 +27,7 @@ report_de <- function(res,
 
   cli::cli_h2("Generating report for differential expression analysis")
 
-  p <- .volcano_plot(
+  p <- volcano_plot(
     dt = res,
     fc_threshold = fc_threshold,
     pval_cutoff = pval_cutoff,
diff --git a/README.Rmd b/README.Rmd
index dfb6753..0d59493 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -28,6 +28,7 @@ knitr::opts_chunk$set(
 [![Manual](https://img.shields.io/badge/manual-passing-brightgreen.svg?style=flat)](https://combiz.github.io/scflow-manual/)
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/combiz/scFlow/issues)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-green.svg)](https://www.gnu.org/licenses/gpl-3.0)
+[![R-CMD-check](https://github.com/combiz/scFlow/workflows/R-CMD-check/badge.svg)](https://github.com/combiz/scFlow/actions)
 <!-- badges: end -->
 
 The goal of scFlow is to provide tools in R to build a complete analysis workflow for single-cell/nuclei RNA sequencing data.
diff --git a/man/cluster_sce.Rd b/man/cluster_sce.Rd
index b7bab05..bf72cb8 100644
--- a/man/cluster_sce.Rd
+++ b/man/cluster_sce.Rd
@@ -9,11 +9,8 @@ cluster_sce(sce, ...)
 \arguments{
 \item{sce}{a SingleCellExperiment object}
 
-\item{...}{see uwot::umap for umap options}
-
-\item{reduction_methods}{one or more of "PCA", "tSNE", "UMAP", "UMAP3D"}
-
-\item{pca_dims}{the number of pca dimensions used}
+\item{...}{see uwot::umap for umap options. Includes reduction_methods one
+or more of "PCA", "tSNE", "UMAP", "UMAP3D"}
 }
 \value{
 sce a SingleCellExperiment object annotated with reducedDims
diff --git a/man/dot-filter_sce_genes_for_de.Rd b/man/dot-filter_sce_genes_for_de.Rd
index 7bf1d59..00c0838 100644
--- a/man/dot-filter_sce_genes_for_de.Rd
+++ b/man/dot-filter_sce_genes_for_de.Rd
@@ -23,7 +23,8 @@ Other differential gene expression:
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{perform_de}()},
 \code{\link{pseudobulk_sce}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
 \keyword{internal}
diff --git a/man/dot-generate_model_from_vars.Rd b/man/dot-generate_model_from_vars.Rd
index c7b6d89..3daff08 100644
--- a/man/dot-generate_model_from_vars.Rd
+++ b/man/dot-generate_model_from_vars.Rd
@@ -39,7 +39,8 @@ Other differential gene expression:
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{perform_de}()},
 \code{\link{pseudobulk_sce}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
 \keyword{internal}
diff --git a/man/dot-perform_de_with_mast.Rd b/man/dot-perform_de_with_mast.Rd
index 05a78d7..025b872 100644
--- a/man/dot-perform_de_with_mast.Rd
+++ b/man/dot-perform_de_with_mast.Rd
@@ -22,7 +22,8 @@ Other differential gene expression:
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{perform_de}()},
 \code{\link{pseudobulk_sce}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
 \keyword{internal}
diff --git a/man/dot-preprocess_sce_for_de.Rd b/man/dot-preprocess_sce_for_de.Rd
index 1e70cd7..321102d 100644
--- a/man/dot-preprocess_sce_for_de.Rd
+++ b/man/dot-preprocess_sce_for_de.Rd
@@ -22,7 +22,8 @@ Other differential gene expression:
 \code{\link{.perform_de_with_mast}()},
 \code{\link{perform_de}()},
 \code{\link{pseudobulk_sce}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
 \keyword{internal}
diff --git a/man/dot-volcano_plot.Rd b/man/dot-volcano_plot.Rd
deleted file mode 100644
index 61f6c37..0000000
--- a/man/dot-volcano_plot.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/diffexp_models.R
-\name{.volcano_plot}
-\alias{.volcano_plot}
-\title{volcano plot}
-\usage{
-.volcano_plot(dt, fc_threshold = 1.05, pval_cutoff = 0.05, n_label = 10)
-}
-\description{
-volcano plot
-}
-\keyword{internal}
diff --git a/man/find_cells.Rd b/man/find_cells.Rd
index 7c371bc..cec2c56 100644
--- a/man/find_cells.Rd
+++ b/man/find_cells.Rd
@@ -29,8 +29,6 @@ the parameter from the top \code{expect_cells} cells (cellranger method).}
 \item{expect_cells}{the number of cells expected for auto retain}
 
 \item{...}{additional arguments for uniformity testing}
-
-\item{alpha}{minimum FDR for \code{\link[DropletUtils:emptyDrops]{DropletUtils::emptyDrops()}}}
 }
 \value{
 sce a SingleCellExperiment object annotated with emptyDrops metrics
diff --git a/man/integrate_sce.Rd b/man/integrate_sce.Rd
index 839e924..f81e198 100644
--- a/man/integrate_sce.Rd
+++ b/man/integrate_sce.Rd
@@ -9,12 +9,11 @@ integrate_sce(sce, method = "Liger", ...)
 \arguments{
 \item{sce}{a SingleCellExperiment object or merged sce objects}
 
-\item{method}{the integration method to use}
-
-\item{...}{Additional arguments}
-
-\item{k}{Inner dimension of factorization (number of factors).
+\item{method}{the integration method to use
 Set to k=30 as default.}
+
+\item{...}{Additional arguments. Such as k Inner dimension of factorization
+(number of factors).}
 }
 \value{
 sce SingleCellExperiment object annotated with reducedDims
diff --git a/man/liger_preprocess.Rd b/man/liger_preprocess.Rd
index ff5e590..6afc823 100644
--- a/man/liger_preprocess.Rd
+++ b/man/liger_preprocess.Rd
@@ -21,10 +21,17 @@ liger_preprocess(
 \arguments{
 \item{sce}{SingleCellExperiment object or merged objects}
 
-\item{k}{Inner dimension of factorization (number of factors).
+\item{k}{Inner dimension of factorization (number of factors).}
+
+\item{unique_id_var}{the colData variable identifying unique samples.
+Default is "manifest".
 
 Make a Liger object:}
 
+\item{take_gene_union}{Whether to fill out raw.data matrices with union
+of genes across all datasets (filling in 0 for missing data)
+(requires make.sparse=T) (default FALSE).}
+
 \item{remove.missing}{Whether to remove cells not expressing any
 measured genes, and genes not
 expressed in any cells (if take.gene.union = T, removes only genes
@@ -32,6 +39,9 @@ not expressed in any dataset) (default TRUE).
 
 Select informative genes:}
 
+\item{num_genes}{Number of genes to find for each dataset.
+Set to 3000 as default.}
+
 \item{combine}{How to combine variable genes across experiments.
 Either "union" or "intersect".
 (default "union")}
@@ -43,14 +53,12 @@ Scale genes by root-mean-square across cells:
 
 Remove cells/genes with no expression across any genes/cells:}
 
-\item{take.gene.union}{Whether to fill out raw.data matrices with union
-of genes across all datasets (filling in 0 for missing data)
-(requires make.sparse=T) (default FALSE).}
+\item{use_cols}{Treat each column as a cell (default TRUE)}
 
-\item{num.genes}{Number of genes to find for each dataset.
-Set to 3000 as default.}
+\item{num_cores}{Number of cores used on user's machine to run function.
+Default fouynd by \code{future::availableCores()}}
 
-\item{use.cols}{Treat each column as a cell (default TRUE)}
+\item{...}{Additional arguments.}
 }
 \value{
 liger preprocessed object.
diff --git a/man/liger_reduce_dims.Rd b/man/liger_reduce_dims.Rd
index 386b0d2..38029c3 100644
--- a/man/liger_reduce_dims.Rd
+++ b/man/liger_reduce_dims.Rd
@@ -50,6 +50,12 @@ this increments the random seed by 1 for each consecutive restart,
 so future factorizations of the same dataset can be run with
 one rep if necessary. (default 1)}
 
+\item{h_init}{Initial values to use for H matrices. (default NULL)}
+
+\item{w_init}{Initial values to use for W matrix (default NULL)}
+
+\item{v_init}{Initial values to use for V matrices (default NULL)}
+
 \item{rand_seed}{Random seed to allow reproducible results (default 1).}
 
 \item{print_obj}{Print objective function values after convergence
@@ -76,11 +82,7 @@ sparse modalities like methylation data). (default FALSE)}
 \item{resolution}{Controls the number of communities detected.
 Higher resolution -> more communities. (default 1)}
 
-\item{H.init}{Initial values to use for H matrices. (default NULL)}
-
-\item{W.init}{Initial values to use for W matrix (default NULL)}
-
-\item{V.init}{Initial values to use for V matrices (default NULL)}
+\item{...}{Additional arguments.}
 }
 \value{
 liger object with H, H.norm, W, and V slots sets.
diff --git a/man/model_celltype_freqs.Rd b/man/model_celltype_freqs.Rd
index 42cdcbd..872adae 100644
--- a/man/model_celltype_freqs.Rd
+++ b/man/model_celltype_freqs.Rd
@@ -25,6 +25,9 @@ model_celltype_freqs(
 
 \item{ref_class}{the class of dependent_var used as reference}
 
+\item{var_order}{Optional re-ordering of subset_group factor levels. Default
+NULL.}
+
 \item{...}{Additional arguments}
 }
 \value{
diff --git a/man/perform_de.Rd b/man/perform_de.Rd
index 8fbbb31..7db7b0e 100644
--- a/man/perform_de.Rd
+++ b/man/perform_de.Rd
@@ -64,6 +64,7 @@ Other differential gene expression:
 \code{\link{.perform_de_with_mast}()},
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{pseudobulk_sce}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
diff --git a/man/plot_expr_by_numeric_var.Rd b/man/plot_expr_by_numeric_var.Rd
index 975e715..89509c3 100644
--- a/man/plot_expr_by_numeric_var.Rd
+++ b/man/plot_expr_by_numeric_var.Rd
@@ -18,6 +18,8 @@ plot_expr_by_numeric_var(
 \arguments{
 \item{sce}{a SingleCellExperiment object}
 
+\item{numeric_var}{The colData variable for x-axis groups. Default is p_tau}
+
 \item{subset_var}{The colData variable to subset on}
 
 \item{subset_group}{The specific subset_var group to subset}
@@ -29,8 +31,6 @@ plot_expr_by_numeric_var(
 \item{size}{point size}
 
 \item{label_angle}{The angle of x-axis labels (e.g. 0, 45)}
-
-\item{group_var}{The colData variable for x-axis groups}
 }
 \value{
 p a ggplot object
diff --git a/man/pseudobulk_sce.Rd b/man/pseudobulk_sce.Rd
index 712f6df..c2cc7c6 100644
--- a/man/pseudobulk_sce.Rd
+++ b/man/pseudobulk_sce.Rd
@@ -38,6 +38,7 @@ Other differential gene expression:
 \code{\link{.perform_de_with_mast}()},
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{perform_de}()},
-\code{\link{report_de}()}
+\code{\link{report_de}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
diff --git a/man/report_de.Rd b/man/report_de.Rd
index 8c04765..a5c3d5a 100644
--- a/man/report_de.Rd
+++ b/man/report_de.Rd
@@ -36,6 +36,7 @@ Other differential gene expression:
 \code{\link{.perform_de_with_mast}()},
 \code{\link{.preprocess_sce_for_de}()},
 \code{\link{perform_de}()},
-\code{\link{pseudobulk_sce}()}
+\code{\link{pseudobulk_sce}()},
+\code{\link{volcano_plot}()}
 }
 \concept{differential gene expression}
diff --git a/man/volcano_plot.Rd b/man/volcano_plot.Rd
new file mode 100644
index 0000000..140b360
--- /dev/null
+++ b/man/volcano_plot.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diffexp_models.R
+\name{volcano_plot}
+\alias{volcano_plot}
+\title{Plot volcano plot for differential expression analysis}
+\usage{
+volcano_plot(dt, fc_threshold = 1.05, pval_cutoff = 0.05, n_label = 10)
+}
+\arguments{
+\item{dt}{Differential expression result table from perform_de() function.}
+
+\item{fc_threshold}{Fold change threshold for the volcano plot. This will be adjusted and plotted as the log2 fold change.  Default is 1.05.}
+
+\item{pval_cutoff}{The adjusted p-value cut-off for the volcano plot. Default is 0.05.}
+
+\item{n_label}{The number of top up & down differentially expressed genes to be labeled. Default is 10.}
+}
+\value{
+No return. The plot is printed out.
+}
+\description{
+Plot volcano plot for differential expression analysis
+}
+\seealso{
+Other differential gene expression: 
+\code{\link{.filter_sce_genes_for_de}()},
+\code{\link{.generate_model_from_vars}()},
+\code{\link{.perform_de_with_mast}()},
+\code{\link{.preprocess_sce_for_de}()},
+\code{\link{perform_de}()},
+\code{\link{pseudobulk_sce}()},
+\code{\link{report_de}()}
+}
+\concept{differential gene expression}