diff --git a/.Rbuildignore b/.Rbuildignore
index a53e219b..f7bd2a92 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -15,4 +15,7 @@
 ^.*\.h5Seurat$
 ^.*\.rds$
 ^.*\.Rds$
+^LICENSE$
 ^data-raw$
+^inst$
+^tests$
diff --git a/DESCRIPTION b/DESCRIPTION
index 8ab1cacc..71ba5959 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 0.0.0.9000
-Date: 2020-08-10
+Version: 4.0.0
+Date: 2021-01-07
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
@@ -17,12 +17,16 @@ Authors@R: c(
 Description: Defines S4 classes for single-cell genomic data and associated
   information, such as dimensionality reduction embeddings, nearest-neighbor
   graphs, and spatially-resolved coordinates. Provides data access methods and
-  R-native hooks to ensure the Seurat object is familiar to other R users.
-URL: http://www.satijalab.org/seurat,
+  R-native hooks to ensure the Seurat object is familiar to other R users. See 
+  Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, 
+  Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, 
+  and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for 
+  more details.
+URL: https://satijalab.org/seurat,
       https://github.com/mojaveazure/seurat-object
 BugReports:
       https://github.com/mojaveazure/seurat-object/issues
-License: GPL-3 | file LICENSE
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1
diff --git a/R/assay.R b/R/assay.R
index d28391a0..cd87c3c1 100644
--- a/R/assay.R
+++ b/R/assay.R
@@ -68,6 +68,8 @@ Assay <- setClass(
 #' @param min.features Include cells where at least this many features are
 #' detected.
 #'
+#' @return A \code{\link{Assay}} object
+#'
 #' @importFrom methods as
 #' @importFrom Matrix colSums rowSums
 #'
@@ -1173,6 +1175,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' calcn <- SeuratObject:::CalcN(pbmc_small[["RNA"]])
@@ -1197,6 +1201,8 @@ CalcN <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 IsSCT <- function(assay) {
   if (is.list(x = assay)) {
     sct.check <- lapply(X = assay, FUN = function(x) {
@@ -1215,6 +1221,8 @@ IsSCT <- function(assay) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 SubsetVST <- function(sct.info, cells, features) {
   cells.keep <- intersect(x = cells, y = rownames(x = sct.info$cell_attr))
   sct.info$cell_attr <- sct.info$cell_attr[cells.keep, ]
@@ -1241,6 +1249,8 @@ SubsetVST <- function(sct.info, cells, features) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 ValidateDataForMerge <- function(assay, slot) {
   mat <- GetAssayData(object = assay, slot = slot)
   if (any(dim(x = mat) == c(0, 0))) {
diff --git a/R/dimreduc.R b/R/dimreduc.R
index 1c028bec..e7e81e52 100644
--- a/R/dimreduc.R
+++ b/R/dimreduc.R
@@ -66,6 +66,8 @@ DimReduc <- setClass(
 #' @param misc list for the user to store any additional information associated
 #' with the dimensional reduction
 #'
+#' @return A \code{\link{DimReduc}} object
+#'
 #' @aliases SetDimReduction
 #'
 #' @export
@@ -777,6 +779,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 Projected <- function(object) {
   return(!IsMatrixEmpty(x = Loadings(object = object, projected = TRUE)))
 }
diff --git a/R/generics.R b/R/generics.R
index 32b31cca..fe38023c 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -10,7 +10,9 @@ NULL
 #' variance). To add cell level information, add to the Seurat object. If adding
 #' feature-level metadata, add to the Assay object (e.g. \code{object[["RNA"]]})
 #'
-#' @inheritParams .AddMetaData
+#' @param object An object
+#' @param metadata A vector, list, or data.frame with metadata to add
+#' @param col.name A name for meta data if not a named list or data.frame
 #'
 #' @return \code{object} with metadata added
 #'
@@ -79,6 +81,8 @@ as.Neighbor <- function(x, ...) {
 #' @param x An object to convert to class \code{Seurat}
 #' @param ... Arguments passed to other methods
 #'
+#' @return A \code{\link{Seurat}} object generated from \code{x}
+#'
 #' @rdname as.Seurat
 #' @export as.Seurat
 #'
@@ -218,6 +222,8 @@ DefaultAssay <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The distance matrix
+#'
 #' @rdname Distances
 #' @export Distances
 #'
@@ -232,6 +238,8 @@ Distances <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The embeddings matrix
+#'
 #' @rdname Embeddings
 #' @export Embeddings
 #'
@@ -475,6 +483,9 @@ IsGlobal <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{JS}: either a \code{\link{JackStrawData}} object or the
+#' specified jackstraw data
+#'
 #' @rdname JS
 #' @export JS
 #'
@@ -486,6 +497,8 @@ JS <- function(object, ...) {
 
 #' @param value JackStraw information
 #'
+#' @return \code{JS<-}: \code{object} with the update jackstraw information
+#'
 #' @rdname JS
 #' @export JS<-
 #'
@@ -498,6 +511,8 @@ JS <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{Key}: the object key
+#'
 #' @rdname Key
 #' @export Key
 #'
@@ -509,6 +524,8 @@ Key <- function(object, ...) {
 
 #' @param value Key value
 #'
+#' @return \code{Key<-}: \code{object} with an updated key
+#'
 #' @rdname Key
 #' @export Key<-
 #'
@@ -523,6 +540,8 @@ Key <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{Loadings}: the feature loadings for \code{object}
+#'
 #' @rdname Loadings
 #' @export Loadings
 #'
@@ -534,6 +553,8 @@ Loadings <- function(object, ...) {
 
 #' @param value Feature loadings to add
 #'
+#' @return \code{Loadings<-}: \code{object} with the updated loadings
+#'
 #' @rdname Loadings
 #' @export Loadings<-
 #'
@@ -724,6 +745,8 @@ StashIdent <- function(object, save.name, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The standard deviations
+#'
 #' @rdname Stdev
 #' @export Stdev
 #'
diff --git a/R/seurat.R b/R/seurat.R
index a0d150e6..c8d492ef 100644
--- a/R/seurat.R
+++ b/R/seurat.R
@@ -2990,6 +2990,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::Collections(pbmc_small)
@@ -3022,6 +3024,8 @@ Collections <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 DefaultImage <- function(object) {
   object <- UpdateSlots(object = object)
   images <- Images(object = object, assay = DefaultAssay(object = object))
@@ -3041,6 +3045,8 @@ DefaultImage <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) {
   object <- UpdateSlots(object = object)
   slots <- na.omit(object = Filter(
@@ -3080,6 +3086,8 @@ FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::FindObject(pbmc_small, name = "RNA")
@@ -3133,6 +3141,8 @@ FindObject <- function(object, name) {
 #'
 #' @seealso \code{\link[sctransform]{get_residuals}}
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' pbmc_small <- SCTransform(pbmc_small, variable.features.n = 20)
@@ -3377,6 +3387,8 @@ GetResidualVstOut <- function(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateAssay <- function(old.assay, assay) {
   cells <- colnames(x = old.assay@data)
   counts <- old.assay@raw.data
@@ -3405,7 +3417,7 @@ UpdateAssay <- function(old.assay, assay) {
 #'
 #' @rdname V2Update
 #'
-#' @keywords internal
+#' @noRd
 #'
 UpdateDimReduction <- function(old.dr, assay) {
   new.dr <- list()
@@ -3453,6 +3465,8 @@ UpdateDimReduction <- function(old.dr, assay) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateJackstraw <- function(old.jackstraw) {
   if (is.null(x = old.jackstraw)) {
     new.jackstraw <- new(
diff --git a/R/spatial.R b/R/spatial.R
index 4481fea1..7379e1c9 100644
--- a/R/spatial.R
+++ b/R/spatial.R
@@ -374,6 +374,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 NullImage <- function(mode = c('grob', 'raster', 'plotly', 'raw')) {
   mode <- mode[1]
   mode <- match.arg(arg = mode)
diff --git a/R/utils.R b/R/utils.R
index 87853f78..1b1c9082 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -321,6 +321,8 @@ S4ToList.list <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 CheckDots <- function(..., fxns = NULL) {
   args.names <- names(x = list(...))
   if (length(x = list(...)) == 0) {
@@ -460,6 +462,8 @@ CheckDots <- function(..., fxns = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 CheckDuplicateCellNames <- function(object.list, verbose = TRUE, stop = FALSE) {
   cell.names <- unlist(x = lapply(X = object.list, FUN = colnames))
   if (any(duplicated(x = cell.names))) {
@@ -497,6 +501,8 @@ CheckDuplicateCellNames <- function(object.list, verbose = TRUE, stop = FALSE) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::ExtractField('Hello World', field = 1, delim = '_')
@@ -526,6 +532,8 @@ ExtractField <- function(string, field = 1, delim = "_") {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::IsMatrixEmpty(new("matrix"))
@@ -553,6 +561,8 @@ IsMatrixEmpty <- function(x) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 IsNullPtr <- function(x) {
   stopifnot(is(object = x, class2 = 'externalptr'))
   return(.Call('isnull', x))
@@ -572,6 +582,8 @@ IsNullPtr <- function(x) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' set.seed(42L)
@@ -608,6 +620,8 @@ RandomName <- function(length = 5L, ...) {
 #'
 #' @seealso \code{\link{s4list}}
 #'
+#' @noRd
+#'
 SwapClassPkg <- function(x, from = NULL, to = NULL) {
   if (!inherits(x = x, what = 'list')) {
     return(x)
@@ -659,6 +673,8 @@ SwapClassPkg <- function(x, from = NULL, to = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 Top <- function(data, num = 20, balanced = FALSE) {
   nr <- nrow(x = data)
   if (num > nr) {
@@ -699,6 +715,8 @@ Top <- function(data, num = 20, balanced = FALSE) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateClassPkg <- function(object, from = NULL, to = NULL) {
   if (!isS4(object)) {
     return(object)
@@ -719,6 +737,8 @@ UpdateClassPkg <- function(object, from = NULL, to = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateSlots <- function(object) {
   object.list <- sapply(
     X = slotNames(x = object),
@@ -759,6 +779,8 @@ UpdateSlots <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateKey <- function(key) {
   if (grepl(pattern = '^[[:alnum:]]+_$', x = key)) {
     return(key)
diff --git a/R/zzz.R b/R/zzz.R
index fff6a20a..4c6c0d32 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -60,6 +60,8 @@ setOldClass(Classes = 'package_version')
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 .AddMetaData <- function(object, metadata, col.name = NULL) {
   if (is.null(x = col.name) && is.atomic(x = metadata)) {
     stop("'col.name' must be provided for atomic metadata types (eg. vectors)")
@@ -88,6 +90,8 @@ setOldClass(Classes = 'package_version')
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 .Misc <- function(object, slot = NULL, ...) {
   CheckDots(...)
   if (is.null(x = slot)) {
@@ -103,6 +107,8 @@ setOldClass(Classes = 'package_version')
 #'
 #' @rdname dot-Misc
 #'
+#' @noRd
+#'
 ".Misc<-" <- function(object, slot, ..., value) {
   CheckDots(...)
   if (slot %in% names(x = Misc(object = object))) {
diff --git a/README.Rmd b/README.Rmd
index 09a65fa9..b285ace0 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -47,8 +47,10 @@ color <- c("experimental" = "orange", "maturing" = "blue", "stable" = "brightgre
 # SeuratObject
 
 <!-- badges: start -->
-[![CRAN/METACRAN](https://img.shields.io/cran/v/`r pkg`)](`r paste0(cran.cannoncial, pkg)`)
 [![Lifecycle](https://img.shields.io/badge/lifecycle-`r stage`-`r color`.svg)](`r github.url`)
+[![CRAN/METACRAN](https://img.shields.io/cran/v/`r pkg`)](`r paste0(cran.cannoncial, pkg)`)
+[![dependencies](https://tinyverse.netlify.com/badge/`r pkg`)](`r paste0(cran.cannoncial, pkg)`)
+[![Downloads](https://cranlogs.r-pkg.org/badges/`r pkg`?color=brightgreen)](`r paste0(cran.cannoncial, pkg)`)
 <!-- badges: end -->
 
 ```{r description, echo=FALSE, results='asis'}
@@ -57,12 +59,8 @@ cat(gsub(pattern = '\n', replacement = ' ', x = description[, "Description"]))
 
 ## Installation
 
-`r pkg` is not currently available on CRAN.
-You can install it from [GitHub](`r github.url`) with:
+`r pkg` is available on CRAN
 
-``` r
-if (!requireNamespace("remotes", quietly = TRUE)) {
-  install.packages("remotes")
-}
-remotes::install_github("mojaveazure/seurat-object")
+```r
+install.packages("SeuratObject")
 ```
diff --git a/README.md b/README.md
index b8035b35..52f85e60 100644
--- a/README.md
+++ b/README.md
@@ -5,24 +5,25 @@
 
 <!-- badges: start -->
 
+[![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://github.com/mojaveazure/seurat-object)
 [![CRAN/METACRAN](https://img.shields.io/cran/v/SeuratObject)](https://cran.r-project.org/package=SeuratObject)
-[![Lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://github.com/mojaveazure/seurat-object)
+[![dependencies](https://tinyverse.netlify.com/badge/SeuratObject)](https://cran.r-project.org/package=SeuratObject)
+[![Downloads](https://cranlogs.r-pkg.org/badges/SeuratObject?color=brightgreen)](https://cran.r-project.org/package=SeuratObject)
 <!-- badges: end -->
 
 Defines S4 classes for single-cell genomic data and associated
 information, such as dimensionality reduction embeddings,
 nearest-neighbor graphs, and spatially-resolved coordinates. Provides
 data access methods and R-native hooks to ensure the Seurat object is
-familiar to other R users.
+familiar to other R users. See Satija R, Farrell J, Gennert D, et al
+(2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015)
+<doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019)
+<doi:10.1016/j.cell.2019.05.031> for more details.
 
 ## Installation
 
-SeuratObject is not currently available on CRAN. You can install it from
-[GitHub](https://github.com/mojaveazure/seurat-object) with:
+SeuratObject is available on CRAN
 
 ``` r
-if (!requireNamespace("remotes", quietly = TRUE)) {
-  install.packages("remotes")
-}
-remotes::install_github("mojaveazure/seurat-object")
+install.packages("SeuratObject")
 ```
diff --git a/cran-comments.md b/cran-comments.md
new file mode 100644
index 00000000..b42113b4
--- /dev/null
+++ b/cran-comments.md
@@ -0,0 +1,18 @@
+# SeuratObject v4.0.0
+
+## Test environments
+* local ubuntu 20.04 install, R 4.0.3
+* local macOS 10.14.6 install, R 4.0.2
+* win-builder (oldrelease, release, devel)
+
+## R CMD check results
+
+There were no ERRORs or WARNINGs
+
+There was 1 NOTE:
+
+* This is a new release.
+
+## Downstream dependencies
+
+There are no packages that import or depend on SeuratObject
diff --git a/man/CalcN.Rd b/man/CalcN.Rd
deleted file mode 100644
index abe09331..00000000
--- a/man/CalcN.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/assay.R
-\name{CalcN}
-\alias{CalcN}
-\title{Calculate nCount and nFeature}
-\usage{
-CalcN(object)
-}
-\arguments{
-\item{object}{An \code{\link{Assay}} object}
-}
-\value{
-A named list with nCount and nFeature
-}
-\description{
-Calculate nCount and nFeature
-}
-\examples{
-\donttest{
-calcn <- SeuratObject:::CalcN(pbmc_small[["RNA"]])
-head(as.data.frame(calcn))
-}
-
-}
-\keyword{internal}
diff --git a/man/CheckDots.Rd b/man/CheckDots.Rd
deleted file mode 100644
index bf366685..00000000
--- a/man/CheckDots.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{CheckDots}
-\alias{CheckDots}
-\title{Check the use of dots}
-\usage{
-CheckDots(..., fxns = NULL)
-}
-\arguments{
-\item{...}{Arguments passed to a function that fall under \code{...}}
-
-\item{fxns}{A list/vector of functions or function names}
-}
-\value{
-...
-}
-\description{
-Check the use of dots
-}
-\keyword{internal}
diff --git a/man/CheckDuplicateCellNames.Rd b/man/CheckDuplicateCellNames.Rd
deleted file mode 100644
index 730b09cd..00000000
--- a/man/CheckDuplicateCellNames.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{CheckDuplicateCellNames}
-\alias{CheckDuplicateCellNames}
-\title{Check a list of objects for duplicate cell names}
-\usage{
-CheckDuplicateCellNames(object.list, verbose = TRUE, stop = FALSE)
-}
-\arguments{
-\item{object.list}{List of Seurat objects}
-
-\item{verbose}{Print message about renaming}
-
-\item{stop}{Error out if any duplicate names exist}
-}
-\value{
-Returns list of objects with duplicate cells renamed to be unique
-}
-\description{
-Check a list of objects for duplicate cell names
-}
-\keyword{internal}
diff --git a/man/Collections.Rd b/man/Collections.Rd
deleted file mode 100644
index 3c14c1b6..00000000
--- a/man/Collections.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{Collections}
-\alias{Collections}
-\title{Object Collections}
-\usage{
-Collections(object)
-}
-\arguments{
-\item{object}{An S4 object}
-}
-\value{
-A vector with the names of slots that are a list
-}
-\description{
-Find the names of collections in an object
-}
-\examples{
-\donttest{
-SeuratObject:::Collections(pbmc_small)
-}
-
-}
-\keyword{internal}
diff --git a/man/CreateAssayObject.Rd b/man/CreateAssayObject.Rd
index 7f83529a..d792d1e5 100644
--- a/man/CreateAssayObject.Rd
+++ b/man/CreateAssayObject.Rd
@@ -18,6 +18,9 @@ new object with a lower cutoff.}
 \item{min.features}{Include cells where at least this many features are
 detected.}
 }
+\value{
+A \code{\link{Assay}} object
+}
 \description{
 Create an Assay object from a feature (e.g. gene) expression matrix. The
 expected format of the input matrix is features x cells.
diff --git a/man/CreateDimReducObject.Rd b/man/CreateDimReducObject.Rd
index 99304a99..812c149a 100644
--- a/man/CreateDimReducObject.Rd
+++ b/man/CreateDimReducObject.Rd
@@ -38,6 +38,9 @@ specific DimReduc}
 \item{misc}{list for the user to store any additional information associated
 with the dimensional reduction}
 }
+\value{
+A \code{\link{DimReduc}} object
+}
 \description{
 Create a DimReduc object
 }
diff --git a/man/DefaultImage.Rd b/man/DefaultImage.Rd
deleted file mode 100644
index c9ca18c0..00000000
--- a/man/DefaultImage.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{DefaultImage}
-\alias{DefaultImage}
-\title{Get the default image of an object}
-\usage{
-DefaultImage(object)
-}
-\arguments{
-\item{object}{A \code{\link{Seurat}} object}
-}
-\value{
-The name of the default image
-}
-\description{
-Attempts to find all images associated with the default assay of the object.
-If none present, finds all images present in the object. Returns the name of
-the first image
-}
-\keyword{internal}
diff --git a/man/Distances.Rd b/man/Distances.Rd
index 1442b3cf..ab74c5b1 100644
--- a/man/Distances.Rd
+++ b/man/Distances.Rd
@@ -14,6 +14,9 @@ Distances(object, ...)
 
 \item{...}{Arguments passed to other methods}
 }
+\value{
+The distance matrix
+}
 \description{
 Get the Neighbor nearest neighbors distance matrix
 }
diff --git a/man/Embeddings.Rd b/man/Embeddings.Rd
index ddbe0eb8..a8e98e18 100644
--- a/man/Embeddings.Rd
+++ b/man/Embeddings.Rd
@@ -19,6 +19,9 @@ Embeddings(object, ...)
 
 \item{reduction}{Name of reduction to pull cell embeddings for}
 }
+\value{
+The embeddings matrix
+}
 \description{
 Get Cell Embeddings
 }
diff --git a/man/ExtractField.Rd b/man/ExtractField.Rd
deleted file mode 100644
index e4137489..00000000
--- a/man/ExtractField.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{ExtractField}
-\alias{ExtractField}
-\title{Extract delimiter information from a string.}
-\usage{
-ExtractField(string, field = 1, delim = "_")
-}
-\arguments{
-\item{string}{String to parse.}
-
-\item{field}{Integer(s) indicating which field(s) to extract. Can be a
-vector multiple numbers.}
-
-\item{delim}{Delimiter to use, set to underscore by default.}
-}
-\value{
-A new string, that parses out the requested fields, and
-(if multiple), rejoins them with the same delimiter
-}
-\description{
-Parses a string (usually a cell name) and extracts fields based
- on a delimiter
-}
-\examples{
-\donttest{
-SeuratObject:::ExtractField('Hello World', field = 1, delim = '_')
-}
-
-}
-\keyword{internal}
diff --git a/man/FilterObjects.Rd b/man/FilterObjects.Rd
deleted file mode 100644
index b72b83a7..00000000
--- a/man/FilterObjects.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{FilterObjects}
-\alias{FilterObjects}
-\title{Get the names of objects within a Seurat object that are of a certain class}
-\usage{
-FilterObjects(object, classes.keep = c("Assay", "DimReduc"))
-}
-\arguments{
-\item{object}{A \code{\link{Seurat}} object}
-
-\item{classes.keep}{A vector of names of classes to get}
-}
-\value{
-A vector with the names of objects within the Seurat object that are
-of class \code{classes.keep}
-}
-\description{
-Get the names of objects within a Seurat object that are of a certain class
-}
-\keyword{internal}
diff --git a/man/FindObject.Rd b/man/FindObject.Rd
deleted file mode 100644
index 3e291021..00000000
--- a/man/FindObject.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{FindObject}
-\alias{FindObject}
-\title{Find the collection of an object within a Seurat object}
-\usage{
-FindObject(object, name)
-}
-\arguments{
-\item{object}{A \code{\link{Seurat}} object}
-
-\item{name}{Name of object to find}
-}
-\value{
-The collection (slot) of the object
-}
-\description{
-Find the collection of an object within a Seurat object
-}
-\examples{
-\donttest{
-SeuratObject:::FindObject(pbmc_small, name = "RNA")
-}
-
-}
-\keyword{internal}
diff --git a/man/GetResidual.Rd b/man/GetResidual.Rd
deleted file mode 100644
index 4c54507b..00000000
--- a/man/GetResidual.Rd
+++ /dev/null
@@ -1,51 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{GetResidual}
-\alias{GetResidual}
-\title{Calculate pearson residuals of features not in the scale.data}
-\usage{
-GetResidual(
-  object,
-  features,
-  assay = "SCT",
-  umi.assay = NULL,
-  clip.range = NULL,
-  replace.value = FALSE,
-  verbose = TRUE
-)
-}
-\arguments{
-\item{object}{A seurat object}
-
-\item{features}{Name of features to add into the scale.data}
-
-\item{assay}{Name of the assay of the seurat object generated by SCTransform}
-
-\item{umi.assay}{Name of the assay of the seurat object containing UMI matrix and the default is
-RNA}
-
-\item{clip.range}{Numeric of length two specifying the min and max values the Pearson residual
-will be clipped to}
-
-\item{replace.value}{Recalculate residuals for all features, even if they are already present.
-Useful if you want to change the clip.range.}
-
-\item{verbose}{Whether to print messages and progress bars}
-}
-\value{
-Returns a Seurat object containing  pearson residuals of added features in its scale.data
-}
-\description{
-This function calls sctransform::get_residuals.
-}
-\examples{
-\dontrun{
-pbmc_small <- SCTransform(pbmc_small, variable.features.n = 20)
-pbmc_small <- GetResidual(pbmc_small, features = c('MS4A1', 'TCL1A'))
-}
-
-}
-\seealso{
-\code{\link[sctransform]{get_residuals}}
-}
-\keyword{internal}
diff --git a/man/IsMatrixEmpty.Rd b/man/IsMatrixEmpty.Rd
deleted file mode 100644
index 3a4ee3d0..00000000
--- a/man/IsMatrixEmpty.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{IsMatrixEmpty}
-\alias{IsMatrixEmpty}
-\title{Check if a matrix is empty}
-\usage{
-IsMatrixEmpty(x)
-}
-\arguments{
-\item{x}{A matrix}
-}
-\value{
-Whether or not \code{x} is empty
-}
-\description{
-Takes a matrix and asks if it's empty (either 0x0 or 1x1 with a value of NA)
-}
-\examples{
-\donttest{
-SeuratObject:::IsMatrixEmpty(new("matrix"))
-SeuratObject:::IsMatrixEmpty(matrix())
-SeuratObject:::IsMatrixEmpty(matrix(1:3))
-}
-
-}
-\keyword{internal}
diff --git a/man/IsNullPtr.Rd b/man/IsNullPtr.Rd
deleted file mode 100644
index c5c3f2dd..00000000
--- a/man/IsNullPtr.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{IsNullPtr}
-\alias{IsNullPtr}
-\title{Test Null Pointers}
-\usage{
-IsNullPtr(x)
-}
-\arguments{
-\item{x}{An \link[methods:externalptr-class]{external pointer} object}
-}
-\value{
-\code{TRUE} if \code{x} is a null pointer, otherwise \code{FALSE}
-}
-\description{
-Check to see if a C++ pointer is a null pointer on the compiled side
-}
-\references{
-\url{https://stackoverflow.com/questions/26666614/how-do-i-check-if-an-externalptr-is-null-from-within-r}
-}
-\keyword{internal}
diff --git a/man/IsSCT.Rd b/man/IsSCT.Rd
deleted file mode 100644
index 0492f2a4..00000000
--- a/man/IsSCT.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/assay.R
-\name{IsSCT}
-\alias{IsSCT}
-\title{Check whether an assay has been processed by sctransform}
-\usage{
-IsSCT(assay)
-}
-\arguments{
-\item{assay}{assay to check}
-}
-\value{
-Boolean
-}
-\description{
-Check whether an assay has been processed by sctransform
-}
-\keyword{internal}
diff --git a/man/JS.Rd b/man/JS.Rd
index 6ccf9230..a165f30f 100644
--- a/man/JS.Rd
+++ b/man/JS.Rd
@@ -31,6 +31,12 @@ JS(object, ...) <- value
 \item{slot}{Name of slot to store JackStraw scores to
 Can shorten to 'empirical', 'fake', 'full', or 'overall'}
 }
+\value{
+\code{JS}: either a \code{\link{JackStrawData}} object or the
+specified jackstraw data
+
+\code{JS<-}: \code{object} with the update jackstraw information
+}
 \description{
 Get and set JackStraw information
 }
diff --git a/man/Key.Rd b/man/Key.Rd
index 0d47b37f..6c4dc04c 100644
--- a/man/Key.Rd
+++ b/man/Key.Rd
@@ -31,6 +31,11 @@ Key(object, ...) <- value
 
 \item{value}{Key value}
 }
+\value{
+\code{Key}: the object key
+
+\code{Key<-}: \code{object} with an updated key
+}
 \description{
 Get and set object keys
 }
diff --git a/man/Loadings.Rd b/man/Loadings.Rd
index 8674150a..dff69d03 100644
--- a/man/Loadings.Rd
+++ b/man/Loadings.Rd
@@ -29,6 +29,11 @@ Loadings(object, ...) <- value
 
 \item{reduction}{Name of reduction to pull feature loadings for}
 }
+\value{
+\code{Loadings}: the feature loadings for \code{object}
+
+\code{Loadings<-}: \code{object} with the updated loadings
+}
 \description{
 Get and set feature loadings
 }
diff --git a/man/NullImage.Rd b/man/NullImage.Rd
deleted file mode 100644
index 78d24c35..00000000
--- a/man/NullImage.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/spatial.R
-\name{NullImage}
-\alias{NullImage}
-\title{Return a null image}
-\usage{
-NullImage(mode = c("grob", "raster", "plotly", "raw"))
-}
-\arguments{
-\item{mode}{How to return the image; should accept one of \dQuote{grob},
-\dQuote{raster}, \dQuote{plotly}, or \dQuote{raw}}
-}
-\value{
-Varies by value of \code{mode}:
-\describe{
- \item{\dQuote{grob}}{a \code{\link[grid]{nullGrob}}}
- \item{\dQuote{raster}}{an empty \code{\link[grDevices:as.raster]{raster}}}
- \item{\dQuote{plotly}}{a list with one named item: \code{value = FALSE}}
- \item{\dQuote{raw}}{returns \code{NULL}}
-}
-}
-\description{
-Return a null image
-}
-\keyword{internal}
diff --git a/man/Projected.Rd b/man/Projected.Rd
deleted file mode 100644
index 8eb8ff3a..00000000
--- a/man/Projected.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dimreduc.R
-\name{Projected}
-\alias{Projected}
-\title{Check to see if projected loadings have been set}
-\usage{
-Projected(object)
-}
-\arguments{
-\item{object}{a DimReduc object}
-}
-\value{
-TRUE if projected loadings have been set, else FALSE
-}
-\description{
-Check to see if projected loadings have been set
-}
-\keyword{internal}
diff --git a/man/RandomName.Rd b/man/RandomName.Rd
deleted file mode 100644
index 723ed177..00000000
--- a/man/RandomName.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{RandomName}
-\alias{RandomName}
-\title{Generate a random name}
-\usage{
-RandomName(length = 5L, ...)
-}
-\arguments{
-\item{length}{How long should the name be}
-
-\item{...}{Extra parameters passed to \code{\link[base]{sample}}}
-}
-\value{
-A character with \code{nchar == length} of randomly sampled letters
-}
-\description{
-Make a name from randomly sampled lowercase letters, pasted together with no
-spaces or other characters
-}
-\examples{
-\dontrun{
-set.seed(42L)
-SeuratObject:::RandomName()
-SeuratObject:::RandomName(7L, replace = TRUE)
-}
-
-}
-\seealso{
-\code{\link[base]{sample}}
-}
-\keyword{internal}
diff --git a/man/SeuratObject-package.Rd b/man/SeuratObject-package.Rd
index e1dd0c78..75f8f7e8 100644
--- a/man/SeuratObject-package.Rd
+++ b/man/SeuratObject-package.Rd
@@ -9,12 +9,16 @@
 Defines S4 classes for single-cell genomic data and associated
   information, such as dimensionality reduction embeddings, nearest-neighbor
   graphs, and spatially-resolved coordinates. Provides data access methods and
-  R-native hooks to ensure the Seurat object is familiar to other R users.
+  R-native hooks to ensure the Seurat object is familiar to other R users. See 
+  Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, 
+  Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, 
+  and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for 
+  more details.
 }
 \seealso{
 Useful links:
 \itemize{
-  \item \url{http://www.satijalab.org/seurat}
+  \item \url{https://satijalab.org/seurat}
   \item \url{https://github.com/mojaveazure/seurat-object}
   \item Report bugs at \url{https://github.com/mojaveazure/seurat-object/issues}
 }
diff --git a/man/Stdev.Rd b/man/Stdev.Rd
index 032dcbb9..97ae554b 100644
--- a/man/Stdev.Rd
+++ b/man/Stdev.Rd
@@ -19,6 +19,9 @@ Stdev(object, ...)
 
 \item{reduction}{Name of reduction to use}
 }
+\value{
+The standard deviations
+}
 \description{
 Get the standard deviations for an object
 }
diff --git a/man/SubsetVST.Rd b/man/SubsetVST.Rd
deleted file mode 100644
index 9cc74eb8..00000000
--- a/man/SubsetVST.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/assay.R
-\name{SubsetVST}
-\alias{SubsetVST}
-\title{Subset cells in vst data}
-\usage{
-SubsetVST(sct.info, cells, features)
-}
-\arguments{
-\item{sct.info}{A vst.out list}
-
-\item{cells}{vector of cells to retain}
-
-\item{features}{vector of features to retain}
-}
-\description{
-Subset cells in vst data
-}
-\keyword{internal}
diff --git a/man/Top.Rd b/man/Top.Rd
deleted file mode 100644
index ae5ff2de..00000000
--- a/man/Top.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{Top}
-\alias{Top}
-\title{Get the top}
-\usage{
-Top(data, num = 20, balanced = FALSE)
-}
-\arguments{
-\item{data}{Data to pull the top from}
-
-\item{num}{Pull top \code{num}}
-
-\item{balanced}{Pull even amounts of from positive and negative values}
-}
-\value{
-The top \code{num}
-}
-\description{
-Get the top
-}
-\keyword{internal}
diff --git a/man/UpdateKey.Rd b/man/UpdateKey.Rd
deleted file mode 100644
index 759ab6ac..00000000
--- a/man/UpdateKey.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{UpdateKey}
-\alias{UpdateKey}
-\title{Update a Key}
-\usage{
-UpdateKey(key)
-}
-\arguments{
-\item{key}{A character to become a Seurat Key}
-}
-\value{
-An updated Key that's valid for Seurat
-}
-\description{
-Update a Key
-}
-\section{\code{Seurat} Object Keys}{
-
-blah
-}
-
-\keyword{internal}
diff --git a/man/UpdateSlots.Rd b/man/UpdateSlots.Rd
deleted file mode 100644
index 8a7a827f..00000000
--- a/man/UpdateSlots.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{UpdateSlots}
-\alias{UpdateSlots}
-\title{Update slots in an object}
-\usage{
-UpdateSlots(object)
-}
-\arguments{
-\item{object}{An object to update}
-}
-\value{
-\code{object} with the latest slot definitions
-}
-\description{
-Update slots in an object
-}
-\keyword{internal}
diff --git a/man/V2Update.Rd b/man/V2Update.Rd
deleted file mode 100644
index 32d2c3d9..00000000
--- a/man/V2Update.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/seurat.R
-\name{V2Update}
-\alias{V2Update}
-\alias{UpdateAssay}
-\alias{UpdateDimReduction}
-\alias{UpdateJackstraw}
-\title{Update Seurat v2 Internal Objects}
-\usage{
-UpdateAssay(old.assay, assay)
-
-UpdateDimReduction(old.dr, assay)
-
-UpdateJackstraw(old.jackstraw)
-}
-\arguments{
-\item{old.assay, old.dr, old.jackstraw}{Seurat v2 assay, dimensional
-reduction, or jackstraw object}
-
-\item{assay}{Name to store for assay in new object}
-
-\item{assay.used}{Name of assay used to compute dimension reduction}
-}
-\value{
-A v3/v4 \code{\link{Assay}}, \code{\link{DimReduc}}, or
-\code{\link{JackStrawData}} object
-}
-\description{
-Helper functions to update old Seurat v2 objects to v3/v4 objects
-}
-\keyword{internal}
diff --git a/man/ValidateDataForMerge.Rd b/man/ValidateDataForMerge.Rd
deleted file mode 100644
index b5bfdf60..00000000
--- a/man/ValidateDataForMerge.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/assay.R
-\name{ValidateDataForMerge}
-\alias{ValidateDataForMerge}
-\title{Validate Assay Data for Merge}
-\usage{
-ValidateDataForMerge(assay, slot)
-}
-\arguments{
-\item{assay}{Assay to pull data from}
-
-\item{slot}{Slot to pull from}
-}
-\value{
-Returns the data matrix if present (i.e.) not 0x0. Otherwise,
-returns an appropriately sized empty sparse matrix
-}
-\description{
-Pulls the proper data matrix for merging assay data. If the slot is empty,
-will return an empty matrix with the proper dimensions from one of the
-remaining data slots.
-}
-\keyword{internal}
diff --git a/man/as.Seurat.Rd b/man/as.Seurat.Rd
index 520932a2..585e25a5 100644
--- a/man/as.Seurat.Rd
+++ b/man/as.Seurat.Rd
@@ -11,6 +11,9 @@ as.Seurat(x, ...)
 
 \item{...}{Arguments passed to other methods}
 }
+\value{
+A \code{\link{Seurat}} object generated from \code{x}
+}
 \description{
 Convert objects to Seurat objects
 }
diff --git a/man/classpkg.Rd b/man/classpkg.Rd
deleted file mode 100644
index e08db104..00000000
--- a/man/classpkg.Rd
+++ /dev/null
@@ -1,48 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{classpkg}
-\alias{classpkg}
-\alias{SwapClassPkg}
-\alias{UpdateClassPkg}
-\title{Update a Class's Package}
-\usage{
-SwapClassPkg(x, from = NULL, to = NULL)
-
-UpdateClassPkg(object, from = NULL, to = NULL)
-}
-\arguments{
-\item{x}{A list with an S4 class definition attribute}
-
-\item{from}{A vector of one or more packages to limit conversion from}
-
-\item{to}{A character naming the package to search for new class definitions;
-defaults to the package of the function calling this function}
-
-\item{object}{An S4 object}
-}
-\value{
-\code{SwapClassPkg}: \code{x} with an updated S4 class
-definition attribute
-
-\code{UpdateClassPkg}: \code{object} with the updated
-class definition
-}
-\description{
-Swap packages for an object's class definition. As classes move between
-packages, these functions rescope the namespace of the S4 class. This allows
-objects to depend only on the new package for class definitions rather than
-both the new and old packages
-}
-\section{S4 Class Definition Attributes}{
-
-S4 classes are scoped to the package and class name. In order to properly
-track which class a list is generated from in order to build a new one,
-these function use an \code{\link[base:attr]{attribute}} to denote the
-class name and package of origin. This attribute is stored as
-\dQuote{classDef} and takes the form of \dQuote{\code{package:class}}.
-}
-
-\seealso{
-\code{\link{s4list}}
-}
-\keyword{internal}
diff --git a/man/dot-AddMetaData.Rd b/man/dot-AddMetaData.Rd
deleted file mode 100644
index 7856e162..00000000
--- a/man/dot-AddMetaData.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/zzz.R
-\name{.AddMetaData}
-\alias{.AddMetaData}
-\title{Object Metadata}
-\usage{
-.AddMetaData(object, metadata, col.name = NULL)
-}
-\arguments{
-\item{object}{An object}
-
-\item{metadata}{A vector, list, or data.frame with metadata to add}
-
-\item{col.name}{A name for meta data if not a named list or data.frame}
-}
-\value{
-object with metadata added
-}
-\description{
-Internal \code{\link{AddMetaData}} definition
-}
-\keyword{internal}
diff --git a/man/dot-Misc.Rd b/man/dot-Misc.Rd
deleted file mode 100644
index c5ea9207..00000000
--- a/man/dot-Misc.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/zzz.R
-\name{.Misc}
-\alias{.Misc}
-\alias{.Misc<-}
-\title{Miscellaneous Data}
-\usage{
-.Misc(object, slot = NULL, ...)
-
-.Misc(object, slot, ...) <- value
-}
-\arguments{
-\item{object}{An object}
-
-\item{slot}{Name of miscellaneous data to get or set}
-
-\item{...}{Arguments passed to other methods}
-
-\item{value}{Data to add}
-}
-\value{
-\code{.Misc}: If \code{slot} is \code{NULL}, all miscellaneous
-data, otherwise the miscellaneous data for \code{slot}
-
-\code{.Misc<-}: \code{object} with \code{value} added to the
-miscellaneous data slot \code{slot}
-}
-\description{
-Internal functions for getting and setting miscellaneous data
-}
-\keyword{internal}