diff --git a/config.yaml b/config.yaml
index 94b86364..29544760 100644
--- a/config.yaml
+++ b/config.yaml
@@ -22,7 +22,7 @@ keywords: 'software, data, lesson, The Carpentries'
 
 # Life cycle stage of the lesson
 # possible values: pre-alpha, alpha, beta, stable
-life_cycle: 'pre-alpha'
+life_cycle: 'beta'
 
 # License of the lesson
 license: 'CC-BY 4.0'
diff --git a/renv/activate.R b/renv/activate.R
index cb5401f9..9b2e7f18 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.3"
+  version <- "1.0.5"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -31,6 +31,14 @@ 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 +58,22 @@ 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")
@@ -1041,7 +1062,7 @@ 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 +1071,7 @@ 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 +1084,14 @@ 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 +1139,14 @@ 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 +1173,7 @@ 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/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
index 614d975c..adc4b3f2 100644
--- a/renv/profiles/lesson-requirements/renv.lock
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.1",
+    "Version": "4.3.2",
     "Repositories": [
       {
         "Name": "BioCsoft",
@@ -61,10 +61,10 @@
     },
     "BH": {
       "Package": "BH",
-      "Version": "1.81.0-1",
+      "Version": "1.84.0-0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
+      "Hash": "a8235afbcd6316e6e91433ea47661013"
     },
     "Biobase": {
       "Package": "Biobase",
@@ -177,14 +177,14 @@
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.1.3",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b2866e62bab9378c3cc9476a1954226b"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "DESeq2": {
       "Package": "DESeq2",
@@ -230,7 +230,7 @@
     },
     "DT": {
       "Package": "DT",
-      "Version": "0.30",
+      "Version": "0.32",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -243,7 +243,7 @@
         "magrittr",
         "promises"
       ],
-      "Hash": "dffb4d94a00be1b4a4507e53ab95bd90"
+      "Hash": "0d3ab8abbb0c3e3daa47d4dc8e17bbae"
     },
     "DelayedArray": {
       "Package": "DelayedArray",
@@ -438,7 +438,7 @@
     },
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-60",
+      "Version": "7.3-60.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -449,11 +449,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "a56a6365b3fa73293ea8d084be0d9bb0"
+      "Hash": "b765b28387acc8ec9e9c1530713cb19c"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.6-1.1",
+      "Version": "1.6-5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -466,7 +466,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "1a00d4828f33a9d690806e98bd17150c"
+      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
     },
     "MatrixGenerics": {
       "Package": "MatrixGenerics",
@@ -500,7 +500,7 @@
     },
     "RCurl": {
       "Package": "RCurl",
-      "Version": "1.98-1.13",
+      "Version": "1.98-1.14",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -508,11 +508,11 @@
         "bitops",
         "methods"
       ],
-      "Hash": "318c7b8d68358b45cbc6115dda23d7db"
+      "Hash": "47f648d288079d0c696804ad4e55197e"
     },
     "RSQLite": {
       "Package": "RSQLite",
-      "Version": "2.3.3",
+      "Version": "2.3.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -524,24 +524,25 @@
         "memoise",
         "methods",
         "pkgconfig",
-        "plogr"
+        "plogr",
+        "rlang"
       ],
-      "Hash": "3de9b130745b42015c060758cf6d9b8d"
+      "Hash": "f5a75d57e0a3014a6ef537ac04a80fc6"
     },
     "Rcpp": {
       "Package": "Rcpp",
-      "Version": "1.0.11",
+      "Version": "1.0.12",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods",
         "utils"
       ],
-      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
     },
     "RcppArmadillo": {
       "Package": "RcppArmadillo",
-      "Version": "0.12.6.6.0",
+      "Version": "0.12.8.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -551,11 +552,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "aabc6cb0f0953d0442d3c82d8a9d2610"
+      "Hash": "e78bbbb81a5dcd71a4bd3268d6ede0b1"
     },
     "RcppEigen": {
       "Package": "RcppEigen",
-      "Version": "0.3.3.9.4",
+      "Version": "0.3.4.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -564,7 +565,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "acb0a5bf38490f26ab8661b467f4f53a"
+      "Hash": "df49e3306f232ec28f1604e36a202847"
     },
     "RcppNumerical": {
       "Package": "RcppNumerical",
@@ -806,7 +807,7 @@
     },
     "bbmle": {
       "Package": "bbmle",
-      "Version": "1.0.25",
+      "Version": "1.0.25.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -821,18 +822,18 @@
         "stats",
         "stats4"
       ],
-      "Hash": "ded471b3be03b4c65419abbc1b5e9f86"
+      "Hash": "f32b6a1dfc5c80504326aa3474b10fe6"
     },
     "bdsmatrix": {
       "Package": "bdsmatrix",
-      "Version": "1.3-6",
+      "Version": "1.3-7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b55d57db210e5af3f097ae228aadaf50"
+      "Hash": "d36e416e5a8f91cf90b5edeb3306703a"
     },
     "bit": {
       "Package": "bit",
@@ -879,7 +880,7 @@
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.5.1",
+      "Version": "0.6.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -890,12 +891,13 @@
         "htmltools",
         "jquerylib",
         "jsonlite",
+        "lifecycle",
         "memoise",
         "mime",
         "rlang",
         "sass"
       ],
-      "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9"
+      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
     },
     "caTools": {
       "Package": "caTools",
@@ -921,7 +923,7 @@
     },
     "circlize": {
       "Package": "circlize",
-      "Version": "0.4.15",
+      "Version": "0.4.16",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -936,18 +938,18 @@
         "stats",
         "utils"
       ],
-      "Hash": "2bb47a2fe6ab009b1dcc5566d8c3a988"
+      "Hash": "bf366c80e2b55a5383b4af8fa2a10b74"
     },
     "cli": {
       "Package": "cli",
-      "Version": "3.6.1",
+      "Version": "3.6.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "89e6d8219950eac806ae0c489052048a"
+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
     },
     "clue": {
       "Package": "clue",
@@ -965,7 +967,7 @@
     },
     "cluster": {
       "Package": "cluster",
-      "Version": "2.1.4",
+      "Version": "2.1.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -975,7 +977,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "5edbbabab6ce0bf7900a74fd4358628e"
+      "Hash": "0aaa05204035dc43ea0004b9c76611dd"
     },
     "clusterProfiler": {
       "Package": "clusterProfiler",
@@ -1005,14 +1007,14 @@
     },
     "coda": {
       "Package": "coda",
-      "Version": "0.19-4",
+      "Version": "0.19-4.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "lattice"
       ],
-      "Hash": "24b6d006b8b2343876cf230687546932"
+      "Hash": "af436915c590afc6fffc3ce3a5be1569"
     },
     "codetools": {
       "Package": "codetools",
@@ -1058,14 +1060,14 @@
     },
     "commonmark": {
       "Package": "commonmark",
-      "Version": "1.9.0",
+      "Version": "1.9.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "d691c61bff84bd63c383874d2d0c3307"
+      "Hash": "5d8225445acb167abf7797de48b2ee3c"
     },
     "cowplot": {
       "Package": "cowplot",
-      "Version": "1.1.1",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1078,17 +1080,17 @@
         "rlang",
         "scales"
       ],
-      "Hash": "b418e8423699d11c7f2087c2bfd07da2"
+      "Hash": "8ef2084dd7d28847b374e55440e4f8cb"
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.4.6",
+      "Version": "0.4.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "707fae4bbf73697ec8d85f9d7076c061"
+      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
     },
     "crayon": {
       "Package": "crayon",
@@ -1104,7 +1106,7 @@
     },
     "crosstalk": {
       "Package": "crosstalk",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1113,39 +1115,39 @@
         "jsonlite",
         "lazyeval"
       ],
-      "Hash": "6aa54f69598c32177e920eb3402e8293"
+      "Hash": "ab12c7b080a57475248a30f4db6298c0"
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.1.0",
+      "Version": "5.2.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "carpentries",
       "Requirements": [
         "R"
       ],
-      "Hash": "9123f3ef96a2c1a93927d828b2fe7d4c"
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.14.8",
+      "Version": "1.15.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b4c06e554f33344e044ccd7fdca750a9"
+      "Hash": "536dfe4ac4093b5d115caed7a1a7223b"
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.33",
+      "Version": "0.6.34",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d"
+      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
     },
     "doParallel": {
       "Package": "doParallel",
@@ -1174,9 +1176,9 @@
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.1.3",
+      "Version": "1.1.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
@@ -1193,7 +1195,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
+      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
     "ellipsis": {
       "Package": "ellipsis",
@@ -1265,7 +1267,7 @@
     },
     "fansi": {
       "Package": "fansi",
-      "Version": "1.0.5",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1273,7 +1275,7 @@
         "grDevices",
         "utils"
       ],
-      "Hash": "3e8583a60163b4bc1a80016e63b9959e"
+      "Hash": "962174cf2aeb5b9eea581522286a911f"
     },
     "farver": {
       "Package": "farver",
@@ -1402,7 +1404,7 @@
     },
     "ggforce": {
       "Package": "ggforce",
-      "Version": "0.4.1",
+      "Version": "0.4.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1427,11 +1429,11 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "a06503f54e227f79b45a72df2946a2d2"
+      "Hash": "384b388bd9155468d2c851846ee69f9f"
     },
     "ggfun": {
       "Package": "ggfun",
-      "Version": "0.1.3",
+      "Version": "0.1.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1442,21 +1444,21 @@
         "rlang",
         "utils"
       ],
-      "Hash": "4657d320971a330ecffd0e1260f58214"
+      "Hash": "91780e07f1d631a1152835b4e25c66b9"
     },
     "ggnewscale": {
       "Package": "ggnewscale",
-      "Version": "0.4.9",
+      "Version": "0.4.10",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "ggplot2"
       ],
-      "Hash": "2d3ce9ca9737ecf195794c63fc40b990"
+      "Hash": "2fb8808f9b9b750371b6bfc4cc9f2939"
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.4",
+      "Version": "3.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1477,7 +1479,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "313d31eff2274ecf4c1d3581db7241f9"
+      "Hash": "52ef83f93f74833007f193b2d4c159a2"
     },
     "ggplotify": {
       "Package": "ggplotify",
@@ -1497,24 +1499,23 @@
     },
     "ggraph": {
       "Package": "ggraph",
-      "Version": "2.1.0",
+      "Version": "2.2.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "MASS",
         "R",
-        "Rcpp",
         "cli",
-        "digest",
+        "cpp11",
         "dplyr",
         "ggforce",
         "ggplot2",
         "ggrepel",
         "graphlayouts",
         "grid",
-        "gtable",
         "igraph",
         "lifecycle",
+        "memoise",
         "rlang",
         "scales",
         "stats",
@@ -1524,11 +1525,11 @@
         "viridis",
         "withr"
       ],
-      "Hash": "62672fd99df5df5814f442e9cd5ec29b"
+      "Hash": "e1758aca79444f8ddf49f745c867c5be"
     },
     "ggrepel": {
       "Package": "ggrepel",
-      "Version": "0.9.4",
+      "Version": "0.9.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1540,7 +1541,7 @@
         "scales",
         "withr"
       ],
-      "Hash": "e9839af82cc43fda486a638b68b439b2"
+      "Hash": "cc3361e234c4a5050e29697d675764aa"
     },
     "ggtree": {
       "Package": "ggtree",
@@ -1571,18 +1572,18 @@
     },
     "glue": {
       "Package": "glue",
-      "Version": "1.6.2",
+      "Version": "1.7.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
     },
     "gplots": {
       "Package": "gplots",
-      "Version": "3.1.3",
+      "Version": "3.1.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1593,11 +1594,11 @@
         "methods",
         "stats"
       ],
-      "Hash": "75437dd4c43599f6e9418ea249495fda"
+      "Hash": "f72b5d1ed587f8905e38ee7295e88d80"
     },
     "graphlayouts": {
       "Package": "graphlayouts",
-      "Version": "1.0.2",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1606,7 +1607,7 @@
         "RcppArmadillo",
         "igraph"
       ],
-      "Hash": "468c98df6feea8aacf159eee906e7ee8"
+      "Hash": "5e9e4cd284ff8abba3cfc43268e3ddd5"
     },
     "gridExtra": {
       "Package": "gridExtra",
@@ -1666,7 +1667,7 @@
     },
     "gtools": {
       "Package": "gtools",
-      "Version": "3.9.4",
+      "Version": "3.9.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1674,7 +1675,7 @@
         "stats",
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