diff --git a/analyses/cell-type-ETP-ALL-03/renv.lock b/analyses/cell-type-ETP-ALL-03/renv.lock
index 7d9ff86bb..8ef69e8a3 100644
--- a/analyses/cell-type-ETP-ALL-03/renv.lock
+++ b/analyses/cell-type-ETP-ALL-03/renv.lock
@@ -211,6 +211,13 @@
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@@ -682,6 +689,18 @@
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@@ -725,6 +744,38 @@
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+      "Requirements": [
+        "R",
+        "Rcpp",
+        "digest",
+        "graphics",
+        "lattice",
+        "methods",
+        "nlme",
+        "parallel",
+        "stats",
+        "utils"
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+        "findpython",
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@@ -861,6 +912,27 @@
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+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
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+        "matrixStats",
+        "methods",
+        "modeltools",
+        "multcomp",
+        "mvtnorm",
+        "parallel",
+        "stats",
+        "stats4",
+        "survival",
+        "utils"
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@@ -989,6 +1061,22 @@
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+      "Source": "Repository",
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+      "Requirements": [
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+        "datasets",
+        "ggplot2",
+        "magrittr",
+        "stats",
+        "utils",
+        "viridis"
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+      "Hash": "735689b7975ad5a4d72b571857d60a33"
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@@ -1014,6 +1102,20 @@
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       "Hash": "e0dff489d999029c03330f063668e590"
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+      "Version": "1.0.17",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "foreach",
+        "iterators",
+        "parallel",
+        "utils"
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+      "Hash": "451e5edf411987991ab6a5410c45011f"
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@@ -1060,6 +1162,23 @@
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       "Hash": "6d7b942d8f615705f89a7883998fc839"
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+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
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+        "Rcpp",
+        "graphics",
+        "limma",
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+        "methods",
+        "stats",
+        "utils"
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+      "Hash": "4c31c0395110252e4ec7cf4ee9cbebb6"
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@@ -1102,6 +1221,16 @@
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+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
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+      "Hash": "2ed9ecb93023f39a449726ed4d43dff8"
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@@ -1109,6 +1238,13 @@
       "Repository": "CRAN",
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+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "8f9aa3ce842296afaad4083b839481a1"
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@@ -1153,6 +1289,19 @@
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@@ -1508,6 +1657,53 @@
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+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
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+        "HiddenMarkov",
+        "Matrix",
+        "R",
+        "RANN",
+        "RColorBrewer",
+        "Seurat",
+        "SingleCellExperiment",
+        "SummarizedExperiment",
+        "ape",
+        "argparse",
+        "caTools",
+        "coda",
+        "coin",
+        "digest",
+        "doParallel",
+        "dplyr",
+        "edgeR",
+        "fastcluster",
+        "fitdistrplus",
+        "foreach",
+        "futile.logger",
+        "future",
+        "ggplot2",
+        "gplots",
+        "grDevices",
+        "graphics",
+        "gridExtra",
+        "igraph",
+        "methods",
+        "parallel",
+        "parallelDist",
+        "phyclust",
+        "reshape2",
+        "rjags",
+        "stats",
+        "tidyr",
+        "utils"
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+      "Hash": "eaf21e1aab39c0b466304b316cc8d031"
+    },
     "irlba": {
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@@ -1532,6 +1728,17 @@
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       "Hash": "0080607b4a1a7b28979aecef976d8bc2"
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+      "Version": "1.0.14",
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+      "Requirements": [
+        "R",
+        "utils"
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+      "Hash": "8954069286b4b2b0d023d1b288dce978"
+    },
     "jquerylib": {
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@@ -1653,6 +1860,18 @@
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       "Hash": "b21c4ae2bb7935504c42bcdf749c04e6"
     },
+    "libcoin": {
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+      "Version": "1.0-10",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "mvtnorm",
+        "stats"
+      ],
+      "Hash": "3f3775a14588ff5d013e5eab4453bf28"
+    },
     "lifecycle": {
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       "Version": "1.0.4",
@@ -1666,6 +1885,22 @@
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       "Hash": "b8552d117e1b808b09a832f589b79035"
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+    "limma": {
+      "Package": "limma",
+      "Version": "3.60.6",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "statmod",
+        "stats",
+        "utils"
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+      "Hash": "0eccf07d5db97b84a912922e1d29e130"
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@@ -1700,6 +1935,17 @@
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       "Hash": "c6fafa6cccb1e1dfe7f7d122efd6e6a7"
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+    "locfit": {
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+      "Version": "1.5-9.10",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "lattice"
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+      "Hash": "7d8e0ac914051ca0254332387d9b5816"
+    },
     "lpSolve": {
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@@ -1816,6 +2062,34 @@
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       "Hash": "2b9414057d7f3725130e2f743ea05a2f"
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+    "modeltools": {
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+      "Version": "0.2-23",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "methods",
+        "stats",
+        "stats4"
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+      "Hash": "f5a957c02222589bdf625a67be68b2a9"
+    },
+    "multcomp": {
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+      "Version": "1.4-26",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "TH.data",
+        "codetools",
+        "graphics",
+        "mvtnorm",
+        "sandwich",
+        "stats",
+        "survival"
+      ],
+      "Hash": "ec6f951a557132215fab91912acdd9ef"
+    },
     "munsell": {
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       "Version": "0.5.1",
@@ -1827,6 +2101,17 @@
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       "Hash": "4fd8900853b746af55b81fda99da7695"
     },
+    "mvtnorm": {
+      "Package": "mvtnorm",
+      "Version": "1.3-2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats"
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+      "Hash": "9e8405eacb262c0a939e121650247f4b"
+    },
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@@ -1917,6 +2202,17 @@
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       "Hash": "51e3a7a4af0b863e5d380575cbd33cda"
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+    "phyclust": {
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+      "Version": "0.1-34",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "ape"
+      ],
+      "Hash": "18a29354ea762dd01042d8697b7089d4"
+    },
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@@ -2076,8 +2372,8 @@
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       "RemoteRepo": "rOpenScPCA",
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-      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
+      "RemoteRef": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
+      "RemoteSha": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
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@@ -2089,7 +2385,7 @@
         "tibble",
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-      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
+      "Hash": "4b9dcd60f9ae2a2e1999acbd49d7b07a"
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@@ -2169,6 +2465,17 @@
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       "Hash": "99e15369f8fb17dc188377234de13fc6"
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+    "rjags": {
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+      "Version": "4-16",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "coda"
+      ],
+      "Hash": "a36ff5b8df160527e29037be8e1cdf7d"
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@@ -2213,6 +2520,19 @@
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+      "Version": "3.1-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils",
+        "zoo"
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+      "Hash": "072bb2d27425f2a58fe71fe1080676ce"
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@@ -2539,6 +2859,18 @@
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+      "Version": "1.5.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "graphics",
+        "stats"
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+      "Hash": "26e158d12052c279bdd4ba858b80fb1f"
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@@ -2709,6 +3041,19 @@
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+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "ggplot2",
+        "gridExtra",
+        "viridisLite"
+      ],
+      "Hash": "acd96d9fa70adeea4a5a1150609b9745"
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diff --git a/analyses/cell-type-nonETP-ALL-03/renv.lock b/analyses/cell-type-nonETP-ALL-03/renv.lock
index 7ddc8099c..7a072e6cc 100644
--- a/analyses/cell-type-nonETP-ALL-03/renv.lock
+++ b/analyses/cell-type-nonETP-ALL-03/renv.lock
@@ -1121,7 +1121,6 @@
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@@ -1130,7 +1129,7 @@
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-      "Hash": "e356046a6ab19635791f7ce46ecd5991"
+      "Hash": "efd05c69dffe1128eb4843f3107eb606"
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@@ -2622,8 +2621,8 @@
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-      "RemoteRef": "main",
-      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
+      "RemoteRef": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
+      "RemoteSha": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
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@@ -2635,7 +2634,7 @@
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-      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
+      "Hash": "4b9dcd60f9ae2a2e1999acbd49d7b07a"
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diff --git a/analyses/hello-clusters/renv.lock b/analyses/hello-clusters/renv.lock
index 5636b53ee..6d9bc52b1 100644
--- a/analyses/hello-clusters/renv.lock
+++ b/analyses/hello-clusters/renv.lock
@@ -1860,8 +1860,8 @@
       "RemoteHost": "api.github.com",
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       "RemoteRepo": "rOpenScPCA",
-      "RemoteRef": "main",
-      "RemoteSha": "fc784446f8d86b072e6f7f67287adfff598f4911",
+      "RemoteRef": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
+      "RemoteSha": "f71a8191130fa543e6506c73c7b62ffa55e8ba3f",
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@@ -1873,7 +1873,7 @@
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-      "Hash": "80a604c3be8af1ae30bcda4f96c4e290"
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