diff --git a/.Rprofile b/.Rprofile
index be1cb7ed..a44306b3 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -1,5 +1,6 @@
-options(BioC_mirror = "https://packagemanager.posit.co/bioconductor")
-options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/config.yaml")
+# Configure BioCManager to use Posit Public Package Manager:
+options(BioC_mirror = "https://p3m.dev/bioconductor")
+options(BIOCONDUCTOR_CONFIG_FILE = "https://p3m.dev/bioconductor/config.yaml")
 
 # activate renv
 source("renv/activate.R")
diff --git a/DESCRIPTION b/DESCRIPTION
index 3c4da22a..334dd28c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,7 +25,7 @@ Description: Tools for processing single cell data associated with the
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends:
     R (>= 4.3.0)
 Imports:
diff --git a/R/build_sce.R b/R/build_sce.R
index 5cd3b277..1cac4da8 100644
--- a/R/build_sce.R
+++ b/R/build_sce.R
@@ -5,15 +5,16 @@
 #'   with intron counts marked by "-U" and ambiguous counts "-A".
 #' @param include_unspliced Whether or not to include the unspliced reads in the counts matrix.
 #'   If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 #'   spliced and unspliced reads.
 #'   Default is TRUE.
 #' @param round_counts Logical indicating in the count matrix should be rounded to integers on import.
 #'   Default is TRUE.
 #'
-#' @return SingleCellExperiment object containing either just a counts assay with spliced cDNA only if
-#'   `include_unspliced` is FALSE. If `include_unspliced` is TRUE, the counts assay will contain both spliced and unspliced
-#'    counts and the spliced assay will contain the counts for just the spliced cDNA.
+#' @return SingleCellExperiment object. If `include_unspliced` is TRUE (default), the counts assay will contain
+#'   both spliced and unspliced counts and the spliced assay will contain the counts for just the spliced cDNA.
+#'   If `include_unspliced` is FALSE, the counts assay will contain spliced cDNA counts only.
+#'
 #'
 #' @examples
 #' \dontrun{
@@ -41,13 +42,13 @@ build_sce <- function(counts,
   # define if counts matrix has any unspliced reads
   has_unspliced <- any(grep("-[IU]$", rownames(counts)))
 
-  if (include_unspliced & !has_unspliced) {
+  if (include_unspliced && !has_unspliced) {
     stop("No counts corresponding to intronic reads detected.
           If `include_unspliced` is TRUE a reference with spliced and unspliced reads must be used.")
   }
 
   # if has unspliced data get counts for both unspliced and spliced
-  if (include_unspliced & has_unspliced) {
+  if (include_unspliced && has_unspliced) {
     total <- collapse_intron_counts(counts, which_counts = c("total"))
     spliced <- collapse_intron_counts(counts, which_counts = c("spliced"))
 
@@ -88,7 +89,7 @@ build_sce <- function(counts,
       counts = total,
       spliced = spliced
     )
-  } else if (!include_unspliced & has_unspliced) {
+  } else if (!include_unspliced && has_unspliced) {
     # still aligned to introns, but want to collapse and just return spliced
     spliced <- collapse_intron_counts(counts, which_counts = c("spliced"))
     assay_list <- list(counts = spliced)
diff --git a/R/import_quant_data.R b/R/import_quant_data.R
index a2b24b8e..324e6d49 100644
--- a/R/import_quant_data.R
+++ b/R/import_quant_data.R
@@ -1,18 +1,19 @@
 #' Import Gene Expression Quantification Data for Single-Cell RNA-Seq
 #'
-#' Imports the gene x cell matrix output from either Alevin, Alevin-fry, Cellranger, or Kallisto and returns a SingleCellExperiment.
+#' Imports the gene x cell matrix output from either Alevin, Alevin-fry, Cell Ranger, or Kallisto
+#'   and returns a SingleCellExperiment.
 #'
 #' @param quant_dir Path to directory where output files are located.
 #' @param tool Type of tool used to create files (alevin, alevin-fry, cellranger, or kallisto).
 #' @param include_unspliced Whether or not to include the unspliced reads in the counts matrix.
 #'   If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 #'   spliced and unspliced reads.
 #'   Default is TRUE.
 #' @param usa_mode Logical indicating if Alevin-fry was used, if the USA mode was invoked.
 #'   Default is FALSE.
 #' @param filter Logical indicating whether or not to filter the counts matrix.
-#'   Filtering is performed using DropletUtils::emptyDrops and cannot be performed with Cellranger.
+#'   Filtering is performed using DropletUtils::emptyDrops and cannot be performed with Cell Ranger.
 #' @param fdr_cutoff FDR cutoff to use for DropletUtils::emptyDrops.
 #'   Default is 0.01.
 #' @param tech_version Technology or kit used to process library (i.e. 10Xv3, 10Xv3.1).
@@ -64,40 +65,22 @@ import_quant_data <- function(quant_dir,
                               ...) {
   which_counts <- match.arg(which_counts)
 
-  if (!(tool %in% c("cellranger", "alevin", "alevin-fry", "kallisto"))) {
-    stop("Tool must be either cellranger, alevin, alevin-fry, or kallisto.")
-  }
-
-  # checks for intron_mode and usa_mode
-  if (!is.logical(include_unspliced)) {
-    stop("include_unspliced must be set as TRUE or FALSE")
-  }
-  if (!is.logical(usa_mode)) {
-    stop("usa_mode must be set as TRUE or FALSE")
-  }
-  if (!is.logical(filter)) {
-    stop("filter must be set as TRUE or FALSE")
-  }
+  stopifnot(
+    "Tool must be one of cellranger, alevin, alevin-fry, or kallisto." =
+      tool %in% c("cellranger", "alevin", "alevin-fry", "kallisto"),
+    "include_unspliced must be set as TRUE or FALSE" = is.logical(include_unspliced),
+    "usa_mode must be set as TRUE or FALSE" = is.logical(usa_mode),
+    "filter must be set as TRUE or FALSE" = is.logical(filter),
+    "USA mode only compatible with alevin-fry." = !(usa_mode && tool %in% c("cellranger", "alevin", "kallisto")),
+    "Include unspliced not compatible with cellranger." = !(include_unspliced && tool %in% c("cellranger")),
+    "Cannot perform emptyDrops filtering on cellranger output." = !(filter && tool == "cellranger")
+  )
 
-  # check that usa_mode and intron_mode are used with the proper tools
-  if (usa_mode & tool %in% c("cellranger", "alevin", "kallisto")) {
-    stop("USA mode only compatible with alevin-fry.")
-  }
-  if (include_unspliced & tool %in% c("cellranger")) {
-    stop("Include unspliced not compatible with cellranger.")
-  }
-
-  # check that filter is not used with cellranger
-  if (filter & tool == "cellranger") {
-    stop("Cannot perform emptyDrops filtering on cellranger output.")
-  }
   if (filter) {
-    if (!(is.numeric(fdr_cutoff))) {
-      stop("fdr_cutoff is not a number.")
-    }
-    if (fdr_cutoff < 0 | fdr_cutoff > 1) {
-      stop("fdr_cutoff must be a number between 0 - 1.")
-    }
+    stopifnot(
+      "fdr_cutoff must be a number." = is.numeric(fdr_cutoff),
+      "fdr_cutoff must be a number between 0 - 1." = fdr_cutoff >= 0 && fdr_cutoff <= 1
+    )
   }
 
   if (tool %in% c("alevin-fry", "alevin")) {
diff --git a/R/merge_sce_list.R b/R/merge_sce_list.R
index 0e65275b..4bb3336a 100644
--- a/R/merge_sce_list.R
+++ b/R/merge_sce_list.R
@@ -160,8 +160,13 @@ merge_sce_list <- function(
       purrr::walk(
         \(altexp_name) {
           sce_list |>
-            purrr::keep(\(sce) altexp_name %in% altExpNames(sce)) |>
-            purrr::map(altExp, altexp_name) |>
+            purrr::map(\(sce) {
+              if (altexp_name %in% altExpNames(sce)) {
+                altExp(sce, altexp_name)
+              }
+            }) |>
+            # remove nulls
+            purrr::keep(\(sce) is(sce, "SingleCellExperiment")) |>
             check_metadata()
         }
       )
@@ -244,24 +249,9 @@ merge_sce_list <- function(
 
   if (include_altexp) {
     for (altexp_name in names(altexp_attributes)) {
-      has_altexp_name <- sce_list |>
-        purrr::map_lgl(\(sce) (altexp_name %in% altExpNames(sce)))
-
-      # For any SCEs without this altExp, create the library_id and sample_id metadata
-      additional_metadata <- sce_list |>
-        purrr::discard(has_altexp_name) |>
-        purrr::map(extract_metadata_for_altexp)
-
       # Update metadata in altExps that were originally present
       altexp_metadata_list <- sce_list |>
-        purrr::keep(has_altexp_name) |>
-        purrr::map(altExp, altexp_name) |>
-        purrr::map(metadata) |>
-        # Tack on the metadata we created for libraries without altExps
-        c(additional_metadata)
-
-      # Ensure correct order
-      altexp_metadata_list <- altexp_metadata_list[names(sce_list)]
+        purrr::map(get_altexp_metadata, altexp_name = altexp_name)
 
       metadata(altExp(merged_sce, altexp_name)) <- prepare_merged_metadata(altexp_metadata_list)
     }
@@ -572,14 +562,27 @@ check_metadata <- function(sce_list, expected_fields = c("library_id", "sample_i
   }
 }
 
-#' Helper function to extract main SCE metadata for inclusion in an altExp
+
+
+#' Helper function to get altExp metadata from an SCE that may not have the altexp
+#' Returns main experiment metadata if the altExp is not present in the SCE
 #'
 #' @param sce SCE object to extract metadata from
+#' @param altexp_name Name of the altExp to extract metadata for
 #'
 #' @return List with fields `library_id` and `sample_id`
-extract_metadata_for_altexp <- function(sce) {
-  list(
-    library_id = metadata(sce)$library_id,
-    sample_id = metadata(sce)$sample_id
-  )
+get_altexp_metadata <- function(sce, altexp_name) {
+  if (altexp_name %in% altExpNames(sce)) {
+    return(
+      metadata(altExp(sce, altexp_name))
+    )
+  } else {
+    # if the altExp is not present, return partial main SCE metadata
+    return(
+      list(
+        library_id = metadata(sce)$library_id,
+        sample_id = metadata(sce)$sample_id
+      )
+    )
+  }
 }
diff --git a/R/read_alevin.R b/R/read_alevin.R
index b9e64052..32e02fbe 100644
--- a/R/read_alevin.R
+++ b/R/read_alevin.R
@@ -7,7 +7,7 @@
 #'   Default is FALSE.
 #' @param include_unspliced Whether or not to include the unspliced reads in the counts matrix.
 #'   If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 #'   spliced and unspliced reads.
 #'   Default is TRUE.
 #' @param feature_data Logical indicating if the data being read in contains feature data.
diff --git a/R/read_cellranger.R b/R/read_cellranger.R
index 7a5f1e41..f546293b 100644
--- a/R/read_cellranger.R
+++ b/R/read_cellranger.R
@@ -1,4 +1,4 @@
-#' Read in counts data processed with Cellranger
+#' Read in counts data processed with Cell Ranger
 #'
 #' @param quant_dir Path to directory where output files are located.
 #'
diff --git a/R/read_kallisto.R b/R/read_kallisto.R
index 1461474a..a4bfa5c2 100644
--- a/R/read_kallisto.R
+++ b/R/read_kallisto.R
@@ -3,7 +3,7 @@
 #' @param quant_dir Path to directory where output files are located.
 #' @param include_unspliced Whether or not to include the unspliced reads in the counts matrix.
 #'   If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+#'   assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 #'   spliced and unspliced reads.
 #'   Default is TRUE.
 #' @param round_counts Logical indicating in the count matrix should be rounded to integers on import.
diff --git a/R/scpcaTools-package.R b/R/scpcaTools-package.R
index 3bc0bbf5..1a039231 100644
--- a/R/scpcaTools-package.R
+++ b/R/scpcaTools-package.R
@@ -1,13 +1,12 @@
 #' scpcaTools: Useful tools for analysis of single-cell RNA seq counts data
 #'
 #' The scpcaTools package contains a set of tools for working with single-cell and single-nuclei RNA-seq counts data.
-#' Mainly, this package can work with data that has been produced using Alevin, Alevin-Fry, Cellranger, or Kallisto.
+#' Mainly, this package can work with data that has been produced using Alevin, Alevin-Fry, Cell Ranger, or Kallisto.
 #'
 #'
-#' @docType package
-#' @name scpcaTools-package
+#' @aliases scpcaTools-package
 #'
 #' @import methods
 #' @import SingleCellExperiment
 #' @import stringr
-NULL
+"_PACKAGE"
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 2307e994..0e003004 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM rocker/r-ver:4.3.2
+FROM rocker/r-ver:4.3.3
 LABEL maintainer="ccdl@alexslemonade.org"
 LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools
 
@@ -13,10 +13,9 @@ RUN Rscript -e "install.packages(c('remotes', 'renv'))"
 
 WORKDIR /usr/local/renv
 COPY renv.lock renv.lock
-# restore with PPM repo set for binary installs
-RUN Rscript -e "renv::consent(provided = TRUE); \
-      renv::restore(repos = 'https://packagemanager.posit.co/cran/latest')" && \
-      rm -rf ~/.local/share/renv && \
+# restore renv and remove cache files
+RUN Rscript -e "renv::restore()" && \
+      rm -rf ~/.cache/R/renv && \
       rm -rf /tmp/downloaded_packages && \
       rm -rf /tmp/Rtmp*
 
@@ -27,7 +26,7 @@ RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonvert
 
 #### Python packages
 COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt && pip cache purge
+RUN pip install --no-cache-dir -r requirements.txt
 
 
 ##########################
diff --git a/docker/renv.lock b/docker/renv.lock
index 99856683..9681d571 100644
--- a/docker/renv.lock
+++ b/docker/renv.lock
@@ -1,46 +1,42 @@
 {
   "R": {
-    "Version": "4.3.1",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "BioCsoft",
-        "URL": "https://packagemanager.posit.co/bioconductor/packages/3.17/bioc"
+        "URL": "https://p3m.dev/bioconductor/packages/3.18/bioc"
       },
       {
         "Name": "BioCann",
-        "URL": "https://packagemanager.posit.co/bioconductor/packages/3.17/data/annotation"
+        "URL": "https://p3m.dev/bioconductor/packages/3.18/data/annotation"
       },
       {
         "Name": "BioCexp",
-        "URL": "https://packagemanager.posit.co/bioconductor/packages/3.17/data/experiment"
+        "URL": "https://p3m.dev/bioconductor/packages/3.18/data/experiment"
       },
       {
         "Name": "BioCworkflows",
-        "URL": "https://packagemanager.posit.co/bioconductor/packages/3.17/workflows"
+        "URL": "https://p3m.dev/bioconductor/packages/3.18/workflows"
       },
       {
         "Name": "BioCbooks",
-        "URL": "https://packagemanager.posit.co/bioconductor/packages/3.17/books"
+        "URL": "https://p3m.dev/bioconductor/packages/3.18/books"
       },
       {
         "Name": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/latest"
+        "URL": "https://p3m.dev/cran/latest"
       }
     ]
   },
   "Bioconductor": {
-    "Version": "3.17"
-  },
-  "Python": {
-    "Version": "3.9.6",
-    "Type": "virtualenv",
-    "Name": "./.venv"
+    "Version": "3.18"
   },
   "Packages": {
     "AnnotationDbi": {
       "Package": "AnnotationDbi",
-      "Version": "1.62.2",
+      "Version": "1.64.1",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "Biobase",
         "BiocGenerics",
@@ -54,12 +50,13 @@
         "stats",
         "stats4"
       ],
-      "Hash": "e6c671413b55490c11402f78889384d9"
+      "Hash": "27587689922e22f60ec9ad0182a0a825"
     },
     "AnnotationFilter": {
       "Package": "AnnotationFilter",
-      "Version": "1.24.0",
+      "Version": "1.26.0",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "GenomicRanges",
         "R",
@@ -67,12 +64,13 @@
         "methods",
         "utils"
       ],
-      "Hash": "5ee6a8b3d2ebe0eff2149c526dda4b64"
+      "Hash": "759acec0b1522c1a85c6ba703d4c0ec5"
     },
     "AnnotationHub": {
       "Package": "AnnotationHub",
-      "Version": "3.8.0",
+      "Version": "3.10.1",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "AnnotationDbi",
         "BiocFileCache",
@@ -91,21 +89,23 @@
         "utils",
         "yaml"
       ],
-      "Hash": "2c1ffa13c06028def99e049e30f5dbfa"
+      "Hash": "07d1966e3ffc8c313410579f76b4718c"
     },
     "BH": {
       "Package": "BH",
-      "Version": "1.81.0-1",
+      "Version": "1.84.0-0",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
+      "Repository": "RSPM",
+      "Hash": "a8235afbcd6316e6e91433ea47661013"
     },
     "BSgenome": {
       "Package": "BSgenome",
-      "Version": "1.68.0",
+      "Version": "1.70.2",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "BiocGenerics",
+        "BiocIO",
         "Biostrings",
         "GenomeInfoDb",
         "GenomicRanges",
@@ -120,11 +120,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "9d7c3c9b904c28bc971ed29d3f3b445e"
+      "Hash": "41a60ca70f713322ca31026f6b9e052b"
     },
     "Biobase": {
       "Package": "Biobase",
-      "Version": "2.60.0",
+      "Version": "2.62.0",
       "Source": "Bioconductor",
       "Requirements": [
         "BiocGenerics",
@@ -132,12 +132,13 @@
         "methods",
         "utils"
       ],
-      "Hash": "ed269b250f5844d54dfdc7e749f901aa"
+      "Hash": "38252a34e82d3ff6bb46b4e2252d2dce"
     },
     "BiocFileCache": {
       "Package": "BiocFileCache",
-      "Version": "2.8.0",
+      "Version": "2.10.2",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "DBI",
         "R",
@@ -151,12 +152,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "4fcebdf379954d5d1a3291006a93499b"
+      "Hash": "d59a927de08cce606299009cc595b2cb"
     },
     "BiocGenerics": {
       "Package": "BiocGenerics",
-      "Version": "0.46.0",
+      "Version": "0.48.1",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "graphics",
@@ -164,11 +166,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "c179ae59955c36f5d0068ed29ce832f7"
+      "Hash": "e34278c65d7dffcc08f737bf0944ca9a"
     },
     "BiocIO": {
       "Package": "BiocIO",
-      "Version": "1.10.0",
+      "Version": "1.12.0",
       "Source": "Bioconductor",
       "Requirements": [
         "BiocGenerics",
@@ -177,7 +179,7 @@
         "methods",
         "tools"
       ],
-      "Hash": "a236af72143f9023b2f9f5f8baa81712"
+      "Hash": "aa543468283543c9a8dad23a4897be96"
     },
     "BiocManager": {
       "Package": "BiocManager",
@@ -191,8 +193,9 @@
     },
     "BiocNeighbors": {
       "Package": "BiocNeighbors",
-      "Version": "1.18.0",
+      "Version": "1.20.2",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "BiocParallel",
         "Matrix",
@@ -202,12 +205,13 @@
         "methods",
         "stats"
       ],
-      "Hash": "54d236313a4df87a45f1a24542df05b8"
+      "Hash": "c5c8ade5852fd3b25c66ec28873d00f1"
     },
     "BiocParallel": {
       "Package": "BiocParallel",
-      "Version": "1.34.2",
+      "Version": "1.36.0",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "BH",
         "R",
@@ -220,12 +224,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "84347b6a8118ba2182b148298b118f0e"
+      "Hash": "6d1689ee8b65614ba6ef4012a67b663a"
     },
     "BiocSingular": {
       "Package": "BiocSingular",
-      "Version": "1.16.0",
+      "Version": "1.18.0",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",
@@ -240,21 +245,23 @@
         "rsvd",
         "utils"
       ],
-      "Hash": "21d431747e4555048f65e6f9f7df8e90"
+      "Hash": "bed2b7ea3b0b0b31387d1d80286abb97"
     },
     "BiocVersion": {
       "Package": "BiocVersion",
-      "Version": "3.17.1",
+      "Version": "3.18.1",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "f7c0d5521799b7b0d0a211143ed0bfcb"
+      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
     },
     "Biostrings": {
       "Package": "Biostrings",
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@@ -3455,9 +3495,9 @@
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@@ -3497,7 +3537,7 @@
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@@ -3531,9 +3571,9 @@
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     "tzdb": {
       "Package": "tzdb",
       "Version": "0.4.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cpp11"
@@ -4529,7 +4571,7 @@
       "Package": "utf8",
       "Version": "1.2.4",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
@@ -4537,19 +4579,19 @@
     },
     "uuid": {
       "Package": "uuid",
-      "Version": "1.1-1",
+      "Version": "1.2-0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "3d78edfb977a69fc7a0341bee25e163f"
+      "Hash": "303c19bfd970bece872f93a824e323d9"
     },
     "uwot": {
       "Package": "uwot",
-      "Version": "0.1.16",
+      "Version": "0.2.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "FNN",
         "Matrix",
@@ -4560,13 +4602,13 @@
         "irlba",
         "methods"
       ],
-      "Hash": "252deaa1c1d6d3da6946694243781ea3"
+      "Hash": "b6020c7a957e9e91b22633fb7821cf9b"
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.6.4",
+      "Version": "0.6.5",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cli",
@@ -4574,38 +4616,38 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "266c1ca411266ba8f365fcc726444b87"
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
     },
     "vipor": {
       "Package": "vipor",
-      "Version": "0.4.5",
+      "Version": "0.4.7",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "graphics",
         "stats"
       ],
-      "Hash": "ea85683da7f2bfa63a98dc6416892591"
+      "Hash": "86493c62c14eb78140f1725003958a77"
     },
     "viridis": {
       "Package": "viridis",
-      "Version": "0.6.4",
+      "Version": "0.6.5",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "ggplot2",
         "gridExtra",
         "viridisLite"
       ],
-      "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1"
+      "Hash": "acd96d9fa70adeea4a5a1150609b9745"
     },
     "viridisLite": {
       "Package": "viridisLite",
       "Version": "0.4.2",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
@@ -4613,9 +4655,9 @@
     },
     "vroom": {
       "Package": "vroom",
-      "Version": "1.6.4",
+      "Version": "1.6.5",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "bit64",
@@ -4635,13 +4677,13 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "9db52c1656cf19c124f93124ea57f0fd"
+      "Hash": "390f9315bc0025be03012054103d227c"
     },
     "waldo": {
       "Package": "waldo",
       "Version": "0.5.2",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cli",
@@ -4655,59 +4697,48 @@
       ],
       "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6"
     },
-    "webshot": {
-      "Package": "webshot",
-      "Version": "0.5.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "callr",
-        "jsonlite",
-        "magrittr"
-      ],
-      "Hash": "16858ee1aba97f902d24049d4a44ef16"
-    },
     "withr": {
       "Package": "withr",
-      "Version": "2.5.2",
+      "Version": "3.0.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "grDevices",
-        "graphics",
-        "stats"
+        "graphics"
       ],
-      "Hash": "4b25e70111b7d644322e9513f403a272"
+      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.43",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
     },
     "xml2": {
       "Package": "xml2",
-      "Version": "1.3.5",
+      "Version": "1.3.6",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
-        "methods"
+        "cli",
+        "methods",
+        "rlang"
       ],
-      "Hash": "6c40e5cfcc6aefd88110666e18c31f40"
+      "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
     },
     "xtable": {
       "Package": "xtable",
       "Version": "1.8-4",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "stats",
@@ -4717,15 +4748,16 @@
     },
     "yaml": {
       "Package": "yaml",
-      "Version": "2.3.7",
+      "Version": "2.3.8",
       "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+      "Repository": "RSPM",
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
     },
     "zellkonverter": {
       "Package": "zellkonverter",
-      "Version": "1.10.1",
+      "Version": "1.12.1",
       "Source": "Bioconductor",
+      "Repository": "RSPM",
       "Requirements": [
         "DelayedArray",
         "Matrix",
@@ -4738,19 +4770,20 @@
         "reticulate",
         "utils"
       ],
-      "Hash": "cd00e53d3e2fe77fff07b933c65de74d"
+      "Hash": "bf5728624cccd09a78363e7b1f4f65e9"
     },
     "zlibbioc": {
       "Package": "zlibbioc",
-      "Version": "1.46.0",
+      "Version": "1.48.2",
       "Source": "Bioconductor",
-      "Hash": "20158ef5adb641f0b4e8d63136f0e870"
+      "Repository": "RSPM",
+      "Hash": "2344be62c2da4d9e9942b5d8db346e59"
     },
     "zoo": {
       "Package": "zoo",
       "Version": "1.8-12",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "grDevices",
diff --git a/inst/WORDLIST b/inst/WORDLIST
index c6387261..e71f36ae 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,15 +1,24 @@
 Alevin
+alevin
 altExp
 altexp
 barcode
+bioconductor
+cDNA
+cellranger
 CMD
 colData
 coldata
 commenter
 Dockerfile
+DropletUtils
+emptyDrops
 Ensembl
 ensembl
+intron
 Kallisto
+kallisto
+LinkingTo
 nf
 pre
 PRs
@@ -22,7 +31,10 @@ SCE's
 SCEs
 ScPCA
 scpca
+scpcaData
 scpcaTools
 SingleCellExperiment
+Spielman
 tidyverse
 unspliced
+vcs
diff --git a/man/build_sce.Rd b/man/build_sce.Rd
index 732ffac6..2ae8b2e6 100644
--- a/man/build_sce.Rd
+++ b/man/build_sce.Rd
@@ -13,7 +13,7 @@ with intron counts marked by "-U" and ambiguous counts "-A".}
 
 \item{include_unspliced}{Whether or not to include the unspliced reads in the counts matrix.
 If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 spliced and unspliced reads.
 Default is TRUE.}
 
@@ -21,9 +21,9 @@ Default is TRUE.}
 Default is TRUE.}
 }
 \value{
-SingleCellExperiment object containing either just a counts assay with spliced cDNA only if
-  `include_unspliced` is FALSE. If `include_unspliced` is TRUE, the counts assay will contain both spliced and unspliced
-   counts and the spliced assay will contain the counts for just the spliced cDNA.
+SingleCellExperiment object. If `include_unspliced` is TRUE (default), the counts assay will contain
+  both spliced and unspliced counts and the spliced assay will contain the counts for just the spliced cDNA.
+  If `include_unspliced` is FALSE, the counts assay will contain spliced cDNA counts only.
 }
 \description{
 Build the SCE object from the counts matrix
diff --git a/man/extract_metadata_for_altexp.Rd b/man/extract_metadata_for_altexp.Rd
deleted file mode 100644
index f7243854..00000000
--- a/man/extract_metadata_for_altexp.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/merge_sce_list.R
-\name{extract_metadata_for_altexp}
-\alias{extract_metadata_for_altexp}
-\title{Helper function to extract main SCE metadata for inclusion in an altExp}
-\usage{
-extract_metadata_for_altexp(sce)
-}
-\arguments{
-\item{sce}{SCE object to extract metadata from}
-}
-\value{
-List with fields `library_id` and `sample_id`
-}
-\description{
-Helper function to extract main SCE metadata for inclusion in an altExp
-}
diff --git a/man/get_altexp_metadata.Rd b/man/get_altexp_metadata.Rd
new file mode 100644
index 00000000..a2b3bd29
--- /dev/null
+++ b/man/get_altexp_metadata.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_sce_list.R
+\name{get_altexp_metadata}
+\alias{get_altexp_metadata}
+\title{Helper function to get altExp metadata from an SCE that may not have the altexp
+Returns main experiment metadata if the altExp is not present in the SCE}
+\usage{
+get_altexp_metadata(sce, altexp_name)
+}
+\arguments{
+\item{sce}{SCE object to extract metadata from}
+
+\item{altexp_name}{Name of the altExp to extract metadata for}
+}
+\value{
+List with fields `library_id` and `sample_id`
+}
+\description{
+Helper function to get altExp metadata from an SCE that may not have the altexp
+Returns main experiment metadata if the altExp is not present in the SCE
+}
diff --git a/man/import_quant_data.Rd b/man/import_quant_data.Rd
index 75469a6d..1d4693bb 100644
--- a/man/import_quant_data.Rd
+++ b/man/import_quant_data.Rd
@@ -22,7 +22,7 @@ import_quant_data(
 
 \item{include_unspliced}{Whether or not to include the unspliced reads in the counts matrix.
 If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 spliced and unspliced reads.
 Default is TRUE.}
 
@@ -30,7 +30,7 @@ Default is TRUE.}
 Default is FALSE.}
 
 \item{filter}{Logical indicating whether or not to filter the counts matrix.
-Filtering is performed using DropletUtils::emptyDrops and cannot be performed with Cellranger.}
+Filtering is performed using DropletUtils::emptyDrops and cannot be performed with Cell Ranger.}
 
 \item{fdr_cutoff}{FDR cutoff to use for DropletUtils::emptyDrops.
 Default is 0.01.}
@@ -43,7 +43,8 @@ Default is 0.01.}
 SingleCellExperiment of unfiltered gene x cell counts matrix
 }
 \description{
-Imports the gene x cell matrix output from either Alevin, Alevin-fry, Cellranger, or Kallisto and returns a SingleCellExperiment.
+Imports the gene x cell matrix output from either Alevin, Alevin-fry, Cell Ranger, or Kallisto
+  and returns a SingleCellExperiment.
 }
 \examples{
 \dontrun{
diff --git a/man/read_alevin.Rd b/man/read_alevin.Rd
index 400e45c9..9ad42556 100644
--- a/man/read_alevin.Rd
+++ b/man/read_alevin.Rd
@@ -27,7 +27,7 @@ Default is FALSE.}
 
 \item{include_unspliced}{Whether or not to include the unspliced reads in the counts matrix.
 If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 spliced and unspliced reads.
 Default is TRUE.}
 
diff --git a/man/read_cellranger.Rd b/man/read_cellranger.Rd
index 94084724..cee6ae25 100644
--- a/man/read_cellranger.Rd
+++ b/man/read_cellranger.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/read_cellranger.R
 \name{read_cellranger}
 \alias{read_cellranger}
-\title{Read in counts data processed with Cellranger}
+\title{Read in counts data processed with Cell Ranger}
 \usage{
 read_cellranger(quant_dir)
 }
@@ -13,7 +13,7 @@ read_cellranger(quant_dir)
 SingleCellExperiment of gene x cell counts matrix
 }
 \description{
-Read in counts data processed with Cellranger
+Read in counts data processed with Cell Ranger
 }
 \examples{
 \dontrun{
diff --git a/man/read_kallisto.Rd b/man/read_kallisto.Rd
index 756e797d..17bbdaac 100644
--- a/man/read_kallisto.Rd
+++ b/man/read_kallisto.Rd
@@ -11,7 +11,7 @@ read_kallisto(quant_dir, include_unspliced = TRUE, round_counts = TRUE)
 
 \item{include_unspliced}{Whether or not to include the unspliced reads in the counts matrix.
 If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced"
-assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference contianing
+assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing
 spliced and unspliced reads.
 Default is TRUE.}
 
diff --git a/man/scpcaTools-package.Rd b/man/scpcaTools-package.Rd
index 0a79283d..a036357c 100644
--- a/man/scpcaTools-package.Rd
+++ b/man/scpcaTools-package.Rd
@@ -2,9 +2,21 @@
 % Please edit documentation in R/scpcaTools-package.R
 \docType{package}
 \name{scpcaTools-package}
+\alias{scpcaTools}
 \alias{scpcaTools-package}
 \title{scpcaTools: Useful tools for analysis of single-cell RNA seq counts data}
 \description{
 The scpcaTools package contains a set of tools for working with single-cell and single-nuclei RNA-seq counts data.
-Mainly, this package can work with data that has been produced using Alevin, Alevin-Fry, Cellranger, or Kallisto.
+Mainly, this package can work with data that has been produced using Alevin, Alevin-Fry, Cell Ranger, or Kallisto.
+}
+\author{
+\strong{Maintainer}: Ally Hawkins \email{ally.hawkins@ccdatalab.org} (0000-0001-6026-3660)
+
+Authors:
+\itemize{
+  \item Joshua A. Shapiro \email{josh.shapiro@ccdatalab.org} (0000-0002-6224-0347)
+  \item Stephanie J. Spielman \email{stephanie.spielman@ccdatalab.org} (0000-0002-9090-4788)
+  \item Chanté J. Bethell (0000-0001-9653-8128)
+}
+
 }
diff --git a/renv/activate.R b/renv/activate.R
index cb5401f9..d13f9932 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.3"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -31,6 +33,14 @@ local({
     if (!is.null(override))
       return(override)
 
+    # if we're being run in a context where R_LIBS is already set,
+    # don't load -- presumably we're being run as a sub-process and
+    # the parent process has already set up library paths for us
+    rcmd <- Sys.getenv("R_CMD", unset = NA)
+    rlibs <- Sys.getenv("R_LIBS", unset = NA)
+    if (!is.na(rlibs) && !is.na(rcmd))
+      return(FALSE)
+
     # next, check environment variables
     # TODO: prefer using the configuration one in the future
     envvars <- c(
@@ -50,9 +60,22 @@ local({
 
   })
 
-  if (!enabled)
+  # bail if we're not enabled
+  if (!enabled) {
+
+    # if we're not enabled, we might still need to manually load
+    # the user profile here
+    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+    if (file.exists(profile)) {
+      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+      if (tolower(cfg) %in% c("true", "t", "1"))
+        sys.source(profile, envir = globalenv())
+    }
+
     return(FALSE)
 
+  }
+
   # avoid recursion
   if (identical(getOption("renv.autoloader.running"), TRUE)) {
     warning("ignoring recursive attempt to run renv autoloader")
@@ -108,6 +131,21 @@ local({
   
   }
   
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+  
+  }
+  
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -610,6 +648,9 @@ local({
   
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
   
@@ -801,24 +842,23 @@ local({
   
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
   
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
   
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
   
     FALSE
@@ -1041,7 +1081,7 @@ local({
     # if jsonlite is loaded, use that instead
     if ("jsonlite" %in% loadedNamespaces()) {
   
-      json <- catch(renv_json_read_jsonlite(file, text))
+      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
       if (!inherits(json, "error"))
         return(json)
   
@@ -1050,7 +1090,7 @@ local({
     }
   
     # otherwise, fall back to the default JSON reader
-    json <- catch(renv_json_read_default(file, text))
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
     if (!inherits(json, "error"))
       return(json)
   
@@ -1063,14 +1103,14 @@ local({
   }
   
   renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
-    text <- paste(text %||% read(file), collapse = "\n")
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
     jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
   }
   
   renv_json_read_default <- function(file = NULL, text = NULL) {
   
     # find strings in the JSON
-    text <- paste(text %||% read(file), collapse = "\n")
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
     pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
     locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
   
@@ -1118,14 +1158,14 @@ local({
     map <- as.list(map)
   
     # remap strings in object
-    remapped <- renv_json_remap(json, map)
+    remapped <- renv_json_read_remap(json, map)
   
     # evaluate
     eval(remapped, envir = baseenv())
   
   }
   
-  renv_json_remap <- function(json, map) {
+  renv_json_read_remap <- function(json, map) {
   
     # fix names
     if (!is.null(names(json))) {
@@ -1152,7 +1192,7 @@ local({
     # recurse
     if (is.recursive(json)) {
       for (i in seq_along(json)) {
-        json[i] <- list(renv_json_remap(json[[i]], map))
+        json[i] <- list(renv_json_read_remap(json[[i]], map))
       }
     }
   
diff --git a/renv/settings.json b/renv/settings.json
index 822d0ed8..60e957b4 100644
--- a/renv/settings.json
+++ b/renv/settings.json
@@ -1,5 +1,5 @@
 {
-  "bioconductor.version": "3.17",
+  "bioconductor.version": "3.18",
   "external.libraries": [],
   "ignored.packages": [
     "scpcaData"
@@ -11,7 +11,7 @@
   ],
   "ppm.enabled": true,
   "ppm.ignored.urls": [],
-  "r.version": "4.3.1",
+  "r.version": "4.3.3",
   "snapshot.type": "implicit",
   "use.cache": true,
   "vcs.ignore.cellar": true,
diff --git a/tests/testthat/test-merge_sce_list.R b/tests/testthat/test-merge_sce_list.R
index f179db53..8dd8bc9a 100644
--- a/tests/testthat/test-merge_sce_list.R
+++ b/tests/testthat/test-merge_sce_list.R
@@ -878,12 +878,12 @@ test_that("check_metadata throws an error when a field is missing", {
   expect_no_error(check_metadata(sce_list, expected_fields = "sample_id"))
 })
 
-test_that("extract_metadata_for_altexp returns the correct values", {
+test_that("get_altexp_metadata returns the correct values", {
   expected_list <- list(
     "library_id" = "library-sce1",
     "sample_id"  = "sample-sce1"
   )
-  observed_list <- extract_metadata_for_altexp(sce_list[[1]])
+  observed_list <- get_altexp_metadata(sce_list[[1]], "MISSING_ALTEXP_NAME")
   expect_equal(observed_list, expected_list)
 })