diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
index e9086f48..4444220e 100644
--- a/renv/profiles/lesson-requirements/renv.lock
+++ b/renv/profiles/lesson-requirements/renv.lock
@@ -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": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "3e0051431dff9acfe66c23765e55c556"
+      "Hash": "9b4993e98e0e19da84c168460c032fef"
     },
     "DESeq2": {
       "Package": "DESeq2",
@@ -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"
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     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.6-4",
+      "Version": "1.6-5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -466,7 +466,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "d9c655b30a2edc6bb2244c1d1e8d549d"
+      "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": "2.3.4",
+      "Version": "2.3.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -527,18 +527,18 @@
         "plogr",
         "rlang"
       ],
-      "Hash": "4bf2af2d714d0ee2b4fec0e6b8c150e6"
+      "Hash": "f5a75d57e0a3014a6ef537ac04a80fc6"
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     "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",
@@ -1007,14 +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",
@@ -1060,14 +1060,14 @@
     },
     "commonmark": {
       "Package": "commonmark",
-      "Version": "1.9.0",
+      "Version": "1.9.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "d691c61bff84bd63c383874d2d0c3307"
+      "Hash": "5d8225445acb167abf7797de48b2ee3c"
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     "cowplot": {
       "Package": "cowplot",
-      "Version": "1.1.2",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1080,7 +1080,7 @@
         "rlang",
         "scales"
       ],
-      "Hash": "ef28211987921217c61b4f4068068dac"
+      "Hash": "8ef2084dd7d28847b374e55440e4f8cb"
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     "cpp11": {
       "Package": "cpp11",
@@ -1121,7 +1121,7 @@
       "Package": "curl",
       "Version": "5.2.0",
       "Source": "Repository",
-      "Repository": "https://carpentries.r-universe.dev",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
@@ -1129,25 +1129,25 @@
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.14.10",
+      "Version": "1.15.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
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-      "Hash": "6ea17a32294d8ca00455825ab0cf71b9"
+      "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a"
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     "digest": {
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-      "Version": "0.6.33",
+      "Version": "0.6.34",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d"
+      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
     },
     "doParallel": {
       "Package": "doParallel",
@@ -1433,7 +1433,7 @@
     },
     "ggfun": {
       "Package": "ggfun",
-      "Version": "0.1.3",
+      "Version": "0.1.4",
       "Source": "Repository",
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@@ -1444,7 +1444,7 @@
         "rlang",
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-      "Hash": "4657d320971a330ecffd0e1260f58214"
+      "Hash": "91780e07f1d631a1152835b4e25c66b9"
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     "ggnewscale": {
       "Package": "ggnewscale",
@@ -1530,7 +1530,7 @@
     },
     "ggrepel": {
       "Package": "ggrepel",
-      "Version": "0.9.4",
+      "Version": "0.9.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1542,7 +1542,7 @@
         "scales",
         "withr"
       ],
-      "Hash": "e9839af82cc43fda486a638b68b439b2"
+      "Hash": "cc3361e234c4a5050e29697d675764aa"
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     "ggtree": {
       "Package": "ggtree",
@@ -1573,18 +1573,18 @@
     },
     "glue": {
       "Package": "glue",
-      "Version": "1.6.2",
+      "Version": "1.7.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
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     "gplots": {
       "Package": "gplots",
-      "Version": "3.1.3",
+      "Version": "3.1.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1595,11 +1595,11 @@
         "methods",
         "stats"
       ],
-      "Hash": "75437dd4c43599f6e9418ea249495fda"
+      "Hash": "f72b5d1ed587f8905e38ee7295e88d80"
     },
     "graphlayouts": {
       "Package": "graphlayouts",
-      "Version": "1.0.2",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1608,7 +1608,7 @@
         "RcppArmadillo",
         "igraph"
       ],
-      "Hash": "468c98df6feea8aacf159eee906e7ee8"
+      "Hash": "5e9e4cd284ff8abba3cfc43268e3ddd5"
     },
     "gridExtra": {
       "Package": "gridExtra",
@@ -1752,9 +1752,9 @@
     },
     "httpuv": {
       "Package": "httpuv",
-      "Version": "1.6.13",
+      "Version": "1.6.14",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "https://carpentries.r-universe.dev",
       "Requirements": [
         "R",
         "R6",
@@ -1763,7 +1763,7 @@
         "promises",
         "utils"
       ],
-      "Hash": "d23d2879001f3d82ee9dc38a9ef53c4c"
+      "Hash": "16abeb167dbf511f8cc0552efaf05bab"
     },
     "httr": {
       "Package": "httr",
@@ -1816,7 +1816,7 @@
     },
     "igraph": {
       "Package": "igraph",
-      "Version": "1.6.0",
+      "Version": "2.0.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1834,7 +1834,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "eef74fe28b747e52288ea9e1d3600034"
+      "Hash": "fb2999614d40fe7fd61cf569b66a2dbc"
     },
     "isoband": {
       "Package": "isoband",
@@ -2167,9 +2167,9 @@
     },
     "patchwork": {
       "Package": "patchwork",
-      "Version": "1.1.3",
+      "Version": "1.2.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "cli",
         "ggplot2",
@@ -2181,7 +2181,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "c5754106c02e8e019941100c81149431"
+      "Hash": "9c8ab14c00ac07e9e04d1664c0b74486"
     },
     "pillar": {
       "Package": "pillar",
@@ -2336,7 +2336,7 @@
     },
     "rintrojs": {
       "Package": "rintrojs",
-      "Version": "0.3.3",
+      "Version": "0.3.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2344,7 +2344,7 @@
         "jsonlite",
         "shiny"
       ],
-      "Hash": "22b1346426a5dbed5725ace115be32ca"
+      "Hash": "e01800bef019328509364ab655fbcca6"
     },
     "rjson": {
       "Package": "rjson",
@@ -2358,14 +2358,14 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.1.2",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "50a6dbdc522936ca35afc5e2082ea91b"
+      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
     },
     "rmarkdown": {
       "Package": "rmarkdown",
@@ -2445,7 +2445,7 @@
     },
     "shadowtext": {
       "Package": "shadowtext",
-      "Version": "0.1.2",
+      "Version": "0.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2454,7 +2454,7 @@
         "grid",
         "scales"
       ],
-      "Hash": "e639c0fa75fc71085c37e21e05a06e41"
+      "Hash": "a6d0947671b22116358e2fa6595abdc4"
     },
     "shape": {
       "Package": "shape",
@@ -2519,7 +2519,7 @@
     },
     "shinyWidgets": {
       "Package": "shinyWidgets",
-      "Version": "0.8.0",
+      "Version": "0.8.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2533,7 +2533,7 @@
         "sass",
         "shiny"
       ],
-      "Hash": "c6acc72327e63668bbc7bd258ee54132"
+      "Hash": "96bb249d21b7473dbeb0311702ef5288"
     },
     "shinydashboard": {
       "Package": "shinydashboard",
@@ -2587,7 +2587,7 @@
       "Package": "stringi",
       "Version": "1.8.3",
       "Source": "Repository",
-      "Repository": "https://carpentries.r-universe.dev",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "stats",
@@ -2652,7 +2652,7 @@
     },
     "tidygraph": {
       "Package": "tidygraph",
-      "Version": "1.3.0",
+      "Version": "1.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2671,11 +2671,11 @@
         "tools",
         "utils"
       ],
-      "Hash": "5c1d6e75684cd37665f7f686dad19510"
+      "Hash": "2149824d406f233b57b087be72c5f163"
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     "tidyr": {
       "Package": "tidyr",
-      "Version": "1.3.0",
+      "Version": "1.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2694,7 +2694,7 @@
         "utils",
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-      "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf"
+      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
     },
     "tidyselect": {
       "Package": "tidyselect",
@@ -2752,7 +2752,7 @@
       "RemoteUsername": "GuangchuangYu",
       "RemoteRepo": "treeio",
       "RemoteRef": "devel",
-      "RemoteSha": "acf29745bd1f98f78ca8e8ab23758c95f65e8086",
+      "RemoteSha": "c58405e2b3959e9e0dff9696a7de01f86fdae6c1",
       "RemoteHost": "api.github.com",
       "Requirements": [
         "R",
@@ -2768,7 +2768,7 @@
         "utils",
         "yulab.utils"
       ],
-      "Hash": "964b4d2d3153b74deb486aace69f802a"
+      "Hash": "c78faf4b992fe20f9f85e66d0af2ba36"
     },
     "tweenr": {
       "Package": "tweenr",
@@ -2823,7 +2823,7 @@
     },
     "viridis": {
       "Package": "viridis",
-      "Version": "0.6.4",
+      "Version": "0.6.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2832,7 +2832,7 @@
         "gridExtra",
         "viridisLite"
       ],
-      "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1"
+      "Hash": "acd96d9fa70adeea4a5a1150609b9745"
     },
     "viridisLite": {
       "Package": "viridisLite",
@@ -2861,16 +2861,15 @@
     },
     "withr": {
       "Package": "withr",
-      "Version": "2.5.2",
+      "Version": "3.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "grDevices",
-        "graphics",
-        "stats"
+        "graphics"
       ],
-      "Hash": "4b25e70111b7d644322e9513f403a272"
+      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
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     "xfun": {
       "Package": "xfun",
@@ -2904,7 +2903,7 @@
     },
     "yulab.utils": {
       "Package": "yulab.utils",
-      "Version": "0.1.2",
+      "Version": "0.1.4",
       "Source": "Repository",
       "Repository": "CRAN",
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@@ -2917,7 +2916,7 @@
         "tools",
         "utils"
       ],
-      "Hash": "b737d549a97343eeebe7b87fa76b53c2"
+      "Hash": "60ee2aaa179dc282e9fa7367bad76e89"
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     "zlibbioc": {
       "Package": "zlibbioc",