diff --git a/DESCRIPTION b/DESCRIPTION
index 5a1f2bf..ffe4fb1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeuratData
 Type: Package
 Title: Install and Manage Seurat Datasets
-Version: 0.1.0
-Date: 2019-07-17
+Version: 0.2.0
+Date: 2019-11-15
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
@@ -18,11 +18,14 @@ License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+Depends:
+    R (>= 3.5.0)
 Imports:
     cli,
     crayon,
+    rappdirs,
     stats,
     utils
-Collate: 
+Collate:
     'zzz.R'
     'seurat_data.R'
diff --git a/NAMESPACE b/NAMESPACE
index bd01537..4b41238 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,6 +3,7 @@
 export(AvailableData)
 export(InstallData)
 export(InstalledData)
+export(LoadData)
 export(RemoveData)
 export(UpdateData)
 importFrom(cli,rule)
@@ -14,8 +15,10 @@ importFrom(crayon,col_nchar)
 importFrom(crayon,green)
 importFrom(crayon,red)
 importFrom(crayon,yellow)
+importFrom(rappdirs,user_data_dir)
 importFrom(stats,na.omit)
 importFrom(utils,available.packages)
+importFrom(utils,data)
 importFrom(utils,install.packages)
 importFrom(utils,packageVersion)
 importFrom(utils,remove.packages)
diff --git a/R/seurat_data.R b/R/seurat_data.R
index ff1743d..c0bfe09 100644
--- a/R/seurat_data.R
+++ b/R/seurat_data.R
@@ -16,7 +16,11 @@ NULL
 #'
 #' @export
 #'
-#' @seealso \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{InstallData}} \code{\link{InstalledData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' AvailableData()
 #'
 AvailableData <- function() {
   UpdateManifest()
@@ -35,10 +39,22 @@ AvailableData <- function() {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstalledData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' \dontrun{
+#' InstallData('pbmc3k')
+#' }
 #'
 InstallData <- function(ds, force.reinstall = FALSE, ...) {
   UpdateManifest()
+  if (pkg.env$source != 'remote') {
+    stop(
+      "No access to remote SeuratData repository, unable to install new datasets",
+      call. = FALSE
+    )
+  }
   pkgs <- NameToPackage(ds = ds)
   if (!force.reinstall) {
     installed <- intersect(x = pkgs, y = rownames(x = InstalledData()))
@@ -46,7 +62,7 @@ InstallData <- function(ds, force.reinstall = FALSE, ...) {
       warning(
         "The following packages are already installed and will not be reinstalled: ",
         paste(
-          gsub(pattern = '\\.SeuratData', replacement = '', x = installed),
+          gsub(pattern = pkg.key, replacement = '', x = installed),
           collapse = ', '
         ),
         call. = FALSE,
@@ -63,7 +79,12 @@ InstallData <- function(ds, force.reinstall = FALSE, ...) {
   for (p in pkgs2[pkgs2 %in% search()]) {
     detach(name = p, unload = TRUE, character.only = TRUE)
   }
-  install.packages(pkgs = pkgs, repos = getOption(x = "SeuratData.repo.use"), type = 'source', ...)
+  install.packages(
+    pkgs = pkgs,
+    repos = getOption(x = "SeuratData.repo.use"),
+    type = 'source',
+    ...
+  )
   for (pkg in pkgs) {
     attachNamespace(ns = pkg)
     pkg.env$attached <- c(pkg.env$attached, pkg)
@@ -86,13 +107,73 @@ InstallData <- function(ds, force.reinstall = FALSE, ...) {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{RemoveData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' InstalledData()
 #'
 InstalledData <- function() {
   dat <- AvailableData()
   return(dat[which(x = dat$Installed, ), , drop = FALSE])
 }
 
+#' Modularly load a dataset
+#'
+#' @inheritParams LoadH5Seurat
+#' @param ds Optional name of dataset to load
+#' @param type How to load the \code{Seurat} object; choose from
+#' \describe{
+#'   \item{info}{Information about the object and what's stored in it}
+#'   \item{raw}{The raw form of the dataset, no other options are evaluated}
+#'   \item{processed}{The proccessed data, modular loading avaible by setting other parameters}
+#' }
+#'
+#' @inherit LoadH5Seurat return
+#'
+#' @importFrom utils data
+#'
+#' @export
+#'
+#' @seealso \code{\link[utils]{data}}
+#'
+LoadData <- function(
+  ds,
+  type = c('info', 'raw', 'processed'),
+  assays = NULL,
+  reductions = NULL,
+  graphs = NULL,
+  verbose = TRUE
+) {
+  .NotYetImplemented()
+  installed <- InstalledData()
+  if (!NameToPackage(ds = ds) %in% rownames(x = installed)) {
+    stop("Cannot find dataset ", ds, call. = FALSE)
+  }
+  ds <- NameToPackage(ds = ds)
+  type <- match.arg(arg = tolower(x = type), choices = c('info', 'raw', 'processed'))
+  if (type == 'raw') {
+    e <- new.env()
+    ds <- gsub(pattern = '\\.SeuratData', replacement = '', x = ds)
+    data(list = ds, envir = e)
+    return(e[[ds]])
+  }
+  .NotYetImplemented()
+  type <- match.arg(arg = type, choices = c('info', 'processed'))
+  return(LoadH5Seurat(
+    file = system.file(
+      file.path('extdata', 'processed.h5Seurat'),
+      package = ds,
+      mustWork = TRUE
+    ),
+    type = ifelse(test = type == 'processed', yes = 'object', no = type),
+    assays = assays,
+    reductions = reductions,
+    graphs = graphs,
+    verbose = verbose
+  ))
+}
+
 #' Remove a dataset
 #'
 #' @inheritParams utils::remove.packages
@@ -102,7 +183,13 @@ InstalledData <- function() {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{UpdateData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{InstalledData}} \code{\link{UpdateData}}
+#'
+#' @examples
+#' \dontrun{
+#' RemoveData('pbmc3k')
+#' }
 #'
 RemoveData <- function(ds, lib) {
   UpdateManifest()
@@ -125,9 +212,22 @@ RemoveData <- function(ds, lib) {
 #'
 #' @export
 #'
-#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}}
+#' @seealso \code{\link{AvailableData}} \code{\link{InstallData}}
+#' \code{\link{InstalledData}} \code{\link{RemoveData}}
+#'
+#' @examples
+#' \dontrun{
+#' UpdateData(ask = FALSE)
+#' }
 #'
 UpdateData <- function(ask = TRUE, lib.loc = NULL) {
+  UpdateManifest()
+  if (pkg.env$source != 'remote') {
+    stop(
+      "No access to remote SeuratData repository, unable to update datasets",
+      call. = FALSE
+    )
+  }
   update.packages(lib.loc = lib.loc, repos = getOption(x = "SeuratData.repo.use"), ask = ask, type = 'source')
   UpdateManifest()
   invisible(x = NULL)
diff --git a/R/zzz.R b/R/zzz.R
index 156cf16..51681a0 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -2,11 +2,19 @@
 #'
 #' @section Package options:
 #'
-#' SeuratData uses the following [options()] to configure behaviour:
+#' SeuratData uses the following options to control behaviour, users can configure
+#' these with \code{\link[base]{options}}:
 #'
 #' \itemize{
 #'   \item `SeuratData.repo.use`: Set the location where the SeuratData datasets
 #'   are stored. Users generally should not modify.
+#'   \item `SeuratData.manifest.cache`: Cache the data manifest whenever we talk
+#'   to the data repository; note, setting to \code{FALSE} will simply prevent
+#'   SeuratData from caching the manifest, not from reading a previously cached
+#'   manifest
+#'   \item `SeuratData.roaming`: For Windows users, use a roaming profile directory
+#'   for domain users. See \url{https://en.wikipedia.org/wiki/Roaming_user_profile}
+#'   for a brief overview and Microsoft's documentation for greater detail
 #' }
 #'
 #' @docType package
@@ -17,16 +25,23 @@
 "_PACKAGE"
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-# Global variables and environment
+# Global variables, default options, and package environment
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 default.options <- list(
-  SeuratData.repo.use = 'https://seurat.nygenome.org'
+  SeuratData.repo.use = 'http://seurat.nygenome.org/',
+  SeuratData.manifest.cache = TRUE,
+  SeuratData.roaming = FALSE
 )
 
+pkg.key <- '\\.SeuratData$'
+
 pkg.env <- new.env()
-pkg.env$manifest <- vector(mode = 'character')
+pkg.env$manifest <- vector(mode = 'list')
+pkg.env$source <- vector(mode = 'character')
+pkg.env$update.call <- vector(mode = 'character')
 pkg.env$attached <- vector(mode = 'character')
+pkg.env$extdata.warn <- FALSE
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # Internal functions
@@ -44,6 +59,12 @@ pkg.env$attached <- vector(mode = 'character')
 #' @author Hadley Wickham
 #' @references \url{https://adv-r.hadley.nz/functions.html#missing-arguments}
 #'
+#' @examples
+#' \dontrun{
+#' 4 %||% 5
+#' NULL %|| 5
+#' }
+#'
 #' @keywords internal
 #'
 `%||%` <- function(lhs, rhs) {
@@ -54,6 +75,28 @@ pkg.env$attached <- vector(mode = 'character')
   }
 }
 
+#' Get an application data directory
+#'
+#' @inheritParams AttachData
+#' @param author Author name for application
+#'
+#' @return A character vector with path to the application data dir
+#'
+#' @importFrom rappdirs user_data_dir
+#'
+#' @seealso \code{\link[rappdirs]{user_data_dir}}
+#'
+#' @keywords internal
+#'
+AppData <- function(pkgname = 'SeuratData', author = pkgname) {
+  return(user_data_dir(
+    appname = pkgname,
+    appauthor = author,
+    version = file.path('%p-platform', '%v'),
+    roaming = getOption(x = 'SeuratData.roaming', default = FALSE)
+  ))
+}
+
 #' Attach datasets
 #'
 #' @param pkgname Name of package
@@ -133,12 +176,99 @@ AttachData <- function(pkgname = 'SeuratData') {
   invisible(x = NULL)
 }
 
+#' Enumerate a list or vector
+#'
+#' @param x A list or a vector
+#'
+#' @return A list of length \code{x} with the following named values:
+#' \describe{
+#'   \item{\code{name}}{The name of \code{x} at a given index}
+#'   \item{\code{value}}{The value of \code{x} at the corresponding index}
+#' }
+#'
+#' @note For any given index \code{i} in \code{x}, all attempts to use the name
+#' of the value of \code{x} at \code{i} will be made. If there is no name
+#' (eg. \code{nchar(x = names(x = x)[i]) == 0}), the index \code{i} will be used
+#' in its stead
+#'
+#' @keywords internal
+#'
+Enumerate <- function(x) {
+  indices <- seq_along(along.with = x)
+  keys <- names(x = x) %||% as.character(x = indices)
+  keys[nchar(x = keys) == 0] <- indices[nchar(x = keys) == 0]
+  vals <- lapply(
+    X = indices,
+    FUN = function(i) {
+      return(c('name' = keys[i], 'value' = unname(obj = x[i])))
+    }
+  )
+  return(vals)
+}
+
+#' Check to see if a matrix is empty
+#'
+#' Deterime if a matrix is empty or not
+#'
+#' @param x A matrix
+#'
+#' @return \code{TRUE} if the matrix is empty otherwise \code{FALSE}
+#'
+#' @details A matrix is considered empty if it satisfies one of the following
+#' conditions:
+#' \itemize{
+#'   \item The dimensions of the matrix are 0-by-0 (\code{all(dim(x) == 0)})
+#'   \item The dimensions of the matrix are 1-by-1 (\code{all(dim(x) == 1)}) and
+#'   the sole value is a \code{NA}
+#' }
+#' These two situations correspond to matrices generated with either
+#' \code{new('matrix')} or \code{matrix()}
+#'
+#' @examples
+#' \dontrun{
+#' IsMatrixEmpty(new('matrix'))
+#' IsMatrixEmpty(matrix())
+#' IsMatrixEmpty(matrix(1:9, nrow = 3))
+#' }
+#'
+#' @keywords internal
+#'
+IsMatrixEmpty <- function(x) {
+  matrix.dims <- dim(x = x)
+  matrix.na <- all(matrix.dims == 1) && all(is.na(x = x))
+  return(all(matrix.dims == 0) || matrix.na)
+}
+
+#' Make a space
+#'
+#' @param n Length space should be
+#'
+#' @return A space (' ') of length \code{n}
+#'
+#' @examples
+#' \dontrun{
+#' MakeSpace(10)
+#' }
+#'
+#' @keywords internal
+#'
+MakeSpace <- function(n) {
+  return(paste(rep_len(x = ' ', length.out = n), collapse = ''))
+}
+
 #' Find dataset packages based on name
 #'
 #' @param ds Names of datasets
 #'
 #' @return A vector of package names based on dataset names
 #'
+#' @examples
+#' \dontrun{
+#' NameToPackage('cbmc')
+#' NameToPackage('pbmc3k.SeuratData')
+#' NameToPackage('notadataset')
+#' }
+#'
 #' @keywords internal
 #'
 NameToPackage <- function(ds) {
@@ -171,77 +301,134 @@ NameToPackage <- function(ds) {
 #' @keywords internal
 #'
 UpdateManifest <- function() {
-  avail.pkgs <- available.packages(
-    repos = getOption(x = "SeuratData.repo.use"),
-    type = 'source',
-    fields = c('Description', 'Title'),
-    ignore_repo_cache = TRUE
+  # Set some defaults
+  pkg.env$source <- 'remote'
+  cache.manifest <- file.path(
+    AppData(pkgname = 'SeuratData', author = 'Satija Lab'),
+    'manifest.Rds'
   )
-  avail.pkgs <- as.data.frame(x = avail.pkgs, stringsAsFactors = FALSE)
-  avail.pkgs <- avail.pkgs[grepl(pattern = '\\.SeuratData$', x = avail.pkgs$Package), , drop = FALSE]
-  avail.pkgs <- apply(
-    X = avail.pkgs,
-    MARGIN = 1,
-    FUN = function(pkg) {
-      dataset <- gsub(
-        pattern = '\\.SeuratData$',
-        replacement = '',
-        x = pkg[['Package']]
-      )
-      desc <- unlist(x = strsplit(x = pkg[['Description']], split = '\n'))
-      desc <- sapply(
-        X = strsplit(x = desc, split = ':'),
-        FUN = function(x) {
-          name <- trimws(x = x[[1]])
-          val <- trimws(x = unlist(x = strsplit(x = x[[2]], split = ',')))
-          val <- paste(val, collapse = ', ')
-          names(x = val) <- name
-          return(val)
-        }
-      )
-      desc <- sapply(
-        X = desc,
-        FUN = function(x) {
-          x <- tryCatch(
-            expr = as.numeric(x = x),
-            warning = function(...) {
-              return(x)
-            }
-          )
-          if (!is.numeric(x = x) && !is.na(x = as.logical(x = x))) {
-            x <- as.logical(x = x)
-          }
-          return(x)
-        },
-        simplify = FALSE,
-        USE.NAMES = TRUE
-      )
-      desc <- c(
-        'Dataset' = dataset,
-        'Version' = pkg[['Version']],
-        'Summary' = pkg[['Title']],
-        desc
+  # Attempt to get the manifest from the remote server
+  avail.pkgs <- tryCatch(
+    expr = available.packages(
+      repos = getOption(x = "SeuratData.repo.use"),
+      type = 'source',
+      fields = c('Description', 'Title'),
+      ignore_repo_cache = TRUE
+    ),
+    warning = function(...) {
+      pkg.env$source <- ifelse(
+        test = file.exists(cache.manifest),
+        yes = 'appdir',
+        no = 'extdata'
       )
-      return(desc)
     }
   )
-  manifest.names <- unique(x = unlist(
-    x = lapply(X = avail.pkgs, FUN = names),
-    use.names = FALSE
-  ))
-  for (pkg in names(x = avail.pkgs)) {
-    for (col in manifest.names) {
-      avail.pkgs[[pkg]][[col]] <- avail.pkgs[[pkg]][[col]] %||% NA
+  # Process the manifest
+  if (pkg.env$source == 'remote') {
+    # Lots of stuff to get the manifest modified from the available.packages format
+    # into something usable by SeuratData
+    pkg.env$extdata.warn <- FALSE
+    avail.pkgs <- as.data.frame(x = avail.pkgs, stringsAsFactors = FALSE)
+    # Ensure we only use datasets tagged with .SeuratData
+    avail.pkgs <- avail.pkgs[grepl(pattern = pkg.key, x = avail.pkgs$Package), , drop = FALSE]
+    # Filter down to dataset name, short summary from package title, and
+    # metadata contained in package description
+    avail.pkgs <- apply(
+      X = avail.pkgs,
+      MARGIN = 1,
+      FUN = function(pkg) {
+        # Get dataset name
+        dataset <- gsub(
+          pattern = pkg.key,
+          replacement = '',
+          x = pkg[['Package']]
+        )
+        # Process the description metadata
+        desc <- unlist(x = strsplit(x = pkg[['Description']], split = '\n'))
+        desc <- sapply(
+          X = strsplit(x = desc, split = ':'),
+          FUN = function(x) {
+            name <- trimws(x = x[[1]])
+            val <- trimws(x = unlist(x = strsplit(x = x[[2]], split = ',')))
+            val <- paste(val, collapse = ', ')
+            names(x = val) <- name
+            return(val)
+          }
+        )
+        desc <- sapply(
+          X = desc,
+          FUN = function(x) {
+            x <- tryCatch(
+              expr = as.numeric(x = x),
+              warning = function(...) {
+                return(x)
+              }
+            )
+            if (!is.numeric(x = x) && !is.na(x = as.logical(x = x))) {
+              x <- as.logical(x = x)
+            }
+            return(x)
+          },
+          simplify = FALSE,
+          USE.NAMES = TRUE
+        )
+        # Assemble the information
+        desc <- c(
+          'Dataset' = dataset,
+          'Version' = pkg[['Version']],
+          'Summary' = pkg[['Title']],
+          desc
+        )
+        return(desc)
+      }
+    )
+    # Pad missing metadata with NAs
+    manifest.names <- unique(x = unlist(
+      x = lapply(X = avail.pkgs, FUN = names),
+      use.names = FALSE
+    ))
+    for (pkg in names(x = avail.pkgs)) {
+      for (col in manifest.names) {
+        avail.pkgs[[pkg]][[col]] <- avail.pkgs[[pkg]][[col]] %||% NA
+      }
     }
+    # Convert each entry to a dataframe and bind everything together
+    avail.pkgs <- lapply(X = avail.pkgs, FUN = as.data.frame, stringsAsFactors = FALSE)
+    avail.pkgs <- do.call(what = 'rbind', args = avail.pkgs)
+    # Coerce version information to package_version
+    avail.pkgs$Version <- package_version(x = avail.pkgs$Version)
+  } else if (pkg.env$source == 'appdir') {
+    # Read cached manifest
+    pkg.env$extdata.warn <- FALSE
+    packageStartupMessage(
+      "Using cached data manifest, last updated at ",
+      file.info(cache.manifest)$ctime
+    )
+    avail.pkgs <- readRDS(file = cache.manifest)
+  } else if (pkg.env$source == 'extdata') {
+    # Read SeuratData-bundled manifest
+    if (!pkg.env$extdata.warn) {
+      warning(
+        "Using SeuratData-bundled data manifest. ",
+        "This may be out-of-date and not contain the latest datasets. ",
+        "This warning will be shown once per session or until we can read from a remote or cached data manifest",
+        call. = FALSE,
+        immediate. = TRUE
+      )
+    }
+    pkg.env$extdata.warn <- TRUE
+    avail.pkgs <- readRDS(file = system.file(
+      'extdata/manifest.Rds',
+      package = 'SeuratData',
+      mustWork = TRUE
+    ))
   }
-  avail.pkgs <- lapply(X = avail.pkgs, FUN = as.data.frame, stringsAsFactors = FALSE)
-  avail.pkgs <- do.call(what = 'rbind', args = avail.pkgs)
-  avail.pkgs$Version <- package_version(x = avail.pkgs$Version)
+  # Get dataset installation status
   avail.pkgs$Installed <- vapply(
     X = rownames(x = avail.pkgs),
     FUN = requireNamespace,
     FUN.VALUE = logical(length = 1L),
-    quietly = TRUE,
+    quietly = TRUE
   )
   avail.pkgs$InstalledVersion <- sapply(
     X = rownames(x = avail.pkgs),
@@ -255,14 +442,33 @@ UpdateManifest <- function() {
       return(as.character(x = pkg.version))
     }
   )
+  # Coerce version information to package_version
+  # Allow NAs to become effectively NA_pacakge_version_
   avail.pkgs$InstalledVersion <- package_version(
     x = avail.pkgs$InstalledVersion,
     strict = FALSE
   )
   # TODO: remove these when we allow loading of processed datasets
-  ds.index <- which(x = colnames(x = avail.pkgs) %in% c('default.dataset', 'other.datasets'))
-  avail.pkgs <- avail.pkgs[, -ds.index]
+  cols.remove <- c('default.dataset', 'other.datasets')
+  if (any(cols.remove %in% colnames(x = avail.pkgs))) {
+    ds.index <- which(x = colnames(x = avail.pkgs) %in% cols.remove)
+    avail.pkgs <- avail.pkgs[, -ds.index]
+  }
   pkg.env$manifest <- avail.pkgs
+  # Cache the manifest
+  if (getOption(x = 'SeuratData.manifest.cache', default = FALSE)) {
+    if (!dir.exists(paths = dirname(path = cache.manifest))) {
+      dir.create(path = dirname(path = cache.manifest), recursive = TRUE)
+    }
+    cached <- if (file.exists(cache.manifest)) {
+      readRDS(file = cache.manifest)
+    } else {
+      NULL
+    }
+    if (!isTRUE(x = all.equal(target = pkg.env$manifest, current = cached))) {
+      saveRDS(object = pkg.env$manifest, file = cache.manifest)
+    }
+  }
   invisible(x = NULL)
 }
 
diff --git a/exec/update_packages.R b/exec/update_packages.R
new file mode 100644
index 0000000..aa1d362
--- /dev/null
+++ b/exec/update_packages.R
@@ -0,0 +1,58 @@
+#!/usr/bin/env Rscript
+
+# Check required packages
+if (!requireNamespace('tools', quietly = TRUE)) {
+  stop("Cannot find the tools package, exiting", call. = FALSE)
+}
+
+# Get the script name
+ProgramName <- function() {
+    prefix <- '--file='
+    name <- sub(
+      pattern = prefix,
+      replacement = '',
+      x = grep(
+        pattern = paste0(prefix, "(.+)"),
+        x = commandArgs(),
+        value = TRUE
+      )
+    )
+    return(name)
+}
+
+# Usage message
+usage <- paste("Usage:", ProgramName(), "/path/to/repo")
+
+# Parse and check arguments
+args <- commandArgs(trailingOnly = TRUE)
+if (length(x = args) != 1 || tolower(x = args) %in% c('-h', '--help')) {
+  cat(usage, '\n', file = stderr())
+  quit(status = 1)
+}
+if (!dir.exists(paths = args)) {
+  stop("Cannot find repo directory ", args, call. = FALSE)
+}
+
+# Get the contrib directories
+dirs <- list.dirs(path = args)
+dirs <- grep(pattern = 'contrib', x = dirs, value = TRUE)
+if (length(x = dirs) < 1) {
+  stop("Invalid repository structure in ", args, call. = FALSE)
+}
+
+# Write the PACKAGES manifests
+for (d in dirs) {
+  type <- if (grepl(pattern = 'macosx', x = d)) {
+    'mac.binary'
+  } else if (grepl(pattern = 'windows', x = d)) {
+    'win.binary'
+  } else {
+    'source'
+  }
+  tools::write_PACKAGES(
+    dir = d,
+    fields = c('Description', 'Title', 'Date'),
+    type = type,
+    verbose = TRUE
+  )
+}
diff --git a/inst/extdata/manifest.Rds b/inst/extdata/manifest.Rds
new file mode 100644
index 0000000..5dda2b0
Binary files /dev/null and b/inst/extdata/manifest.Rds differ
diff --git a/man/AppData.Rd b/man/AppData.Rd
new file mode 100644
index 0000000..eefc803
--- /dev/null
+++ b/man/AppData.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{AppData}
+\alias{AppData}
+\title{Get an application data directory}
+\usage{
+AppData(pkgname = "SeuratData", author = pkgname)
+}
+\arguments{
+\item{pkgname}{Name of package}
+
+\item{author}{Author name for application}
+}
+\value{
+A character vector with path to the application data dir
+}
+\description{
+Get an application data directory
+}
+\seealso{
+\code{\link[rappdirs]{user_data_dir}}
+}
+\keyword{internal}
diff --git a/man/AvailableData.Rd b/man/AvailableData.Rd
index 2526a4d..ac06af4 100644
--- a/man/AvailableData.Rd
+++ b/man/AvailableData.Rd
@@ -19,7 +19,12 @@ Other columns are extra metadata, and may change as new datasets are made availa
 }
 \description{
 Get list of available datasets
+}
+\examples{
+AvailableData()
+
 }
 \seealso{
-\code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+\code{\link{InstallData}} \code{\link{InstalledData}}
+\code{\link{RemoveData}} \code{\link{UpdateData}}
 }
diff --git a/man/Enumerate.Rd b/man/Enumerate.Rd
new file mode 100644
index 0000000..2e95974
--- /dev/null
+++ b/man/Enumerate.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{Enumerate}
+\alias{Enumerate}
+\title{Enumerate a list or vector}
+\usage{
+Enumerate(x)
+}
+\arguments{
+\item{x}{A list or a vector}
+}
+\value{
+A list of length \code{x} with the following named values:
+\describe{
+  \item{\code{name}}{The name of \code{x} at a given index}
+  \item{\code{value}}{The value of \code{x} at the corresponding index}
+}
+}
+\description{
+Enumerate a list or vector
+}
+\note{
+For any given index \code{i} in \code{x}, all attempts to use the name
+of the value of \code{x} at \code{i} will be made. If there is no name
+(eg. \code{nchar(x = names(x = x)[i]) == 0}), the index \code{i} will be used
+in its stead
+}
+\keyword{internal}
diff --git a/man/InstallData.Rd b/man/InstallData.Rd
index 5018550..cf79746 100644
--- a/man/InstallData.Rd
+++ b/man/InstallData.Rd
@@ -18,7 +18,14 @@ Invisible \code{NULL}
 }
 \description{
 Install a dataset
+}
+\examples{
+\dontrun{
+InstallData('pbmc3k')
+}
+
 }
 \seealso{
-\code{\link{AvailableData}} \code{\link{InstalledData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+\code{\link{AvailableData}} \code{\link{InstalledData}}
+\code{\link{RemoveData}} \code{\link{UpdateData}}
 }
diff --git a/man/InstalledData.Rd b/man/InstalledData.Rd
index 74852ce..24d6f89 100644
--- a/man/InstalledData.Rd
+++ b/man/InstalledData.Rd
@@ -19,7 +19,12 @@ Other columns are extra metadata, and may change as new datasets are made availa
 }
 \description{
 Get a list of installed datasets
+}
+\examples{
+InstalledData()
+
 }
 \seealso{
-\code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{RemoveData}} \code{\link{UpdateData}}
+\code{\link{AvailableData}} \code{\link{InstallData}}
+\code{\link{RemoveData}} \code{\link{UpdateData}}
 }
diff --git a/man/IsMatrixEmpty.Rd b/man/IsMatrixEmpty.Rd
new file mode 100644
index 0000000..acd15c3
--- /dev/null
+++ b/man/IsMatrixEmpty.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{IsMatrixEmpty}
+\alias{IsMatrixEmpty}
+\title{Check to see if a matrix is empty}
+\usage{
+IsMatrixEmpty(x)
+}
+\arguments{
+\item{x}{A matrix}
+}
+\value{
+\code{TRUE} if the matrix is empty otherwise \code{FALSE}
+}
+\description{
+Deterime if a matrix is empty or not
+}
+\details{
+A matrix is considered empty if it satisfies one of the following
+conditions:
+\itemize{
+  \item The dimensions of the matrix are 0-by-0 (\code{all(dim(x) == 0)})
+  \item The dimensions of the matrix are 1-by-1 (\code{all(dim(x) == 1)}) and
+  the sole value is a \code{NA}
+}
+These two situations correspond to matrices generated with either
+\code{new('matrix')} or \code{matrix()}
+}
+\examples{
+\dontrun{
+IsMatrixEmpty(new('matrix'))
+IsMatrixEmpty(matrix())
+IsMatrixEmpty(matrix(1:9, nrow = 3))
+}
+
+}
+\keyword{internal}
diff --git a/man/LoadData.Rd b/man/LoadData.Rd
new file mode 100644
index 0000000..e3ca9a5
--- /dev/null
+++ b/man/LoadData.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/seurat_data.R
+\name{LoadData}
+\alias{LoadData}
+\title{Modularly load a dataset}
+\usage{
+LoadData(ds, type = c("info", "raw", "processed"), assays = NULL,
+  reductions = NULL, graphs = NULL, verbose = TRUE)
+}
+\arguments{
+\item{ds}{Optional name of dataset to load}
+
+\item{type}{How to load the \code{Seurat} object; choose from
+\describe{
+  \item{info}{Information about the object and what's stored in it}
+  \item{raw}{The raw form of the dataset, no other options are evaluated}
+  \item{processed}{The proccessed data, modular loading avaible by setting other parameters}
+}}
+}
+\description{
+Modularly load a dataset
+}
+\seealso{
+\code{\link[utils]{data}}
+}
diff --git a/man/MakeSpace.Rd b/man/MakeSpace.Rd
new file mode 100644
index 0000000..0f3a6eb
--- /dev/null
+++ b/man/MakeSpace.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{MakeSpace}
+\alias{MakeSpace}
+\title{Make a space}
+\usage{
+MakeSpace(n)
+}
+\arguments{
+\item{n}{Length space should be}
+}
+\value{
+A space (' ') of length \code{n}
+}
+\description{
+Make a space
+}
+\examples{
+\dontrun{
+MakeSpace(10)
+}
+
+}
+\keyword{internal}
diff --git a/man/NameToPackage.Rd b/man/NameToPackage.Rd
index 92a3d14..af9d743 100644
--- a/man/NameToPackage.Rd
+++ b/man/NameToPackage.Rd
@@ -14,5 +14,13 @@ A vector of package names based on dataset names
 }
 \description{
 Find dataset packages based on name
+}
+\examples{
+\dontrun{
+NameToPackage('cbmc')
+NameToPackage('pbmc3k.SeuratData')
+NameToPackage('notadataset')
+}
+
 }
 \keyword{internal}
diff --git a/man/RemoveData.Rd b/man/RemoveData.Rd
index 2f5e21e..57433e5 100644
--- a/man/RemoveData.Rd
+++ b/man/RemoveData.Rd
@@ -15,7 +15,14 @@ RemoveData(ds, lib)
 }
 \description{
 Remove a dataset
+}
+\examples{
+\dontrun{
+RemoveData('pbmc3k')
+}
+
 }
 \seealso{
-\code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{UpdateData}}
+\code{\link{AvailableData}} \code{\link{InstallData}}
+\code{\link{InstalledData}} \code{\link{UpdateData}}
 }
diff --git a/man/SeuratData-package.Rd b/man/SeuratData-package.Rd
index 9036e29..18498c2 100644
--- a/man/SeuratData-package.Rd
+++ b/man/SeuratData-package.Rd
@@ -14,11 +14,19 @@ Single cell RNA sequencing datasets can be large, consisting of matrices
 \section{Package options}{
 
 
-SeuratData uses the following [options()] to configure behaviour:
+SeuratData uses the following options to control behaviour, users can configure
+these with \code{\link[base]{options}}:
 
 \itemize{
   \item `SeuratData.repo.use`: Set the location where the SeuratData datasets
   are stored. Users generally should not modify.
+  \item `SeuratData.manifest.cache`: Cache the data manifest whenever we talk
+  to the data repository; note, setting to \code{FALSE} will simply prevent
+  SeuratData from caching the manifest, not from reading a previously cached
+  manifest
+  \item `SeuratData.roaming`: For Windows users, use a roaming profile directory
+  for domain users. See \url{https://en.wikipedia.org/wiki/Roaming_user_profile}
+  for a brief overview and Microsoft's documentation for greater detail
 }
 }
 
diff --git a/man/UpdateData.Rd b/man/UpdateData.Rd
index ccdf2d2..f389c41 100644
--- a/man/UpdateData.Rd
+++ b/man/UpdateData.Rd
@@ -25,7 +25,14 @@ Invisible \code{NULL}
 }
 \description{
 Update datasets
+}
+\examples{
+\dontrun{
+UpdateData(ask = FALSE)
+}
+
 }
 \seealso{
-\code{\link{AvailableData}} \code{\link{InstallData}} \code{\link{InstalledData}} \code{\link{RemoveData}}
+\code{\link{AvailableData}} \code{\link{InstallData}}
+\code{\link{InstalledData}} \code{\link{RemoveData}}
 }
diff --git a/man/set-if-null.Rd b/man/set-if-null.Rd
index 4db00db..0de9104 100644
--- a/man/set-if-null.Rd
+++ b/man/set-if-null.Rd
@@ -17,6 +17,13 @@ rhs if lhs is null, else lhs
 }
 \description{
 Set a default value if an object is null
+}
+\examples{
+\dontrun{
+4 \%||\% 5
+NULL \%|| 5
+}
+
 }
 \references{
 \url{https://adv-r.hadley.nz/functions.html#missing-arguments}