From 0b1136d314af5487118034395f8bb12927e3fa43 Mon Sep 17 00:00:00 2001
From: Emma Rand <emma.rand@york.ac.uk>
Date: Fri, 13 Oct 2023 13:05:23 +0100
Subject: [PATCH] update lock file

---
 renv.lock | 342 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 342 insertions(+)

diff --git a/renv.lock b/renv.lock
index 18f7ed3..9fff535 100644
--- a/renv.lock
+++ b/renv.lock
@@ -2,6 +2,26 @@
   "R": {
     "Version": "4.3.1",
     "Repositories": [
+      {
+        "Name": "BioCsoft",
+        "URL": "https://bioconductor.org/packages/3.17/bioc"
+      },
+      {
+        "Name": "BioCann",
+        "URL": "https://bioconductor.org/packages/3.17/data/annotation"
+      },
+      {
+        "Name": "BioCexp",
+        "URL": "https://bioconductor.org/packages/3.17/data/experiment"
+      },
+      {
+        "Name": "BioCworkflows",
+        "URL": "https://bioconductor.org/packages/3.17/workflows"
+      },
+      {
+        "Name": "BioCbooks",
+        "URL": "https://bioconductor.org/packages/3.17/books"
+      },
       {
         "Name": "CRAN",
         "URL": "https://packagemanager.posit.co/cran/latest"
@@ -54,6 +74,21 @@
       ],
       "Hash": "d57e43105a1aa9cb54fdb4629725acb1"
     },
+    "BiocNeighbors": {
+      "Package": "BiocNeighbors",
+      "Version": "1.18.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocParallel",
+        "Matrix",
+        "Rcpp",
+        "RcppHNSW",
+        "S4Vectors",
+        "methods",
+        "stats"
+      ],
+      "Hash": "54d236313a4df87a45f1a24542df05b8"
+    },
     "BiocParallel": {
       "Package": "BiocParallel",
       "Version": "1.34.2",
@@ -72,6 +107,26 @@
       ],
       "Hash": "84347b6a8118ba2182b148298b118f0e"
     },
+    "BiocSingular": {
+      "Package": "BiocSingular",
+      "Version": "1.16.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocGenerics",
+        "BiocParallel",
+        "DelayedArray",
+        "Matrix",
+        "Rcpp",
+        "S4Vectors",
+        "ScaledMatrix",
+        "beachmat",
+        "irlba",
+        "methods",
+        "rsvd",
+        "utils"
+      ],
+      "Hash": "21d431747e4555048f65e6f9f7df8e90"
+    },
     "BiocVersion": {
       "Package": "BiocVersion",
       "Version": "3.17.1",
@@ -132,6 +187,22 @@
       ],
       "Hash": "ef6ff3e15ce624118e6cf8151e58e38c"
     },
+    "DelayedMatrixStats": {
+      "Package": "DelayedMatrixStats",
+      "Version": "1.22.6",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "DelayedArray",
+        "IRanges",
+        "Matrix",
+        "MatrixGenerics",
+        "S4Vectors",
+        "matrixStats",
+        "methods",
+        "sparseMatrixStats"
+      ],
+      "Hash": "126ad3bc49aefe4565670c2c16f50bd2"
+    },
     "GenomeInfoDb": {
       "Package": "GenomeInfoDb",
       "Version": "1.36.4",
@@ -290,6 +361,17 @@
       ],
       "Hash": "cafeccdc6577a445a15ce98b6a1805cf"
     },
+    "RcppHNSW": {
+      "Package": "RcppHNSW",
+      "Version": "0.5.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Rcpp",
+        "methods"
+      ],
+      "Hash": "6af2d9ed44e0281f6ae77eb6bed7a3c9"
+    },
     "S4Arrays": {
       "Package": "S4Arrays",
       "Version": "1.0.6",
@@ -321,6 +403,34 @@
       ],
       "Hash": "338207894998073e7823706f886a1386"
     },
+    "ScaledMatrix": {
+      "Package": "ScaledMatrix",
+      "Version": "1.8.1",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "DelayedArray",
+        "Matrix",
+        "S4Vectors",
+        "methods"
+      ],
+      "Hash": "57301723a70d0ee3c7d53691681fade0"
+    },
+    "SingleCellExperiment": {
+      "Package": "SingleCellExperiment",
+      "Version": "1.22.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocGenerics",
+        "DelayedArray",
+        "GenomicRanges",
+        "S4Vectors",
+        "SummarizedExperiment",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "47569baf7560bf8e3ba57386e9672f7f"
+    },
     "SummarizedExperiment": {
       "Package": "SummarizedExperiment",
       "Version": "1.30.2",
@@ -415,6 +525,19 @@
       ],
       "Hash": "543776ae6848fde2f48ff3816d0628bc"
     },
+    "beachmat": {
+      "Package": "beachmat",
+      "Version": "2.16.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocGenerics",
+        "DelayedArray",
+        "Matrix",
+        "Rcpp",
+        "methods"
+      ],
+      "Hash": "43616288aada4bfe6fd316435445cfb1"
+    },
     "bit": {
       "Package": "bit",
       "Version": "4.0.5",
@@ -458,6 +581,24 @@
       ],
       "Hash": "40415719b5a479b87949f3aa0aee737c"
     },
+    "bluster": {
+      "Package": "bluster",
+      "Version": "1.10.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocNeighbors",
+        "BiocParallel",
+        "Matrix",
+        "Rcpp",
+        "S4Vectors",
+        "cluster",
+        "igraph",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "49d6795461d47f4c1a1d1d35ecc91b7a"
+    },
     "broom": {
       "Package": "broom",
       "Version": "1.0.5",
@@ -571,6 +712,20 @@
       ],
       "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
     },
+    "cluster": {
+      "Package": "cluster",
+      "Version": "2.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "stats",
+        "utils"
+      ],
+      "Hash": "5edbbabab6ce0bf7900a74fd4358628e"
+    },
     "codetools": {
       "Package": "codetools",
       "Version": "0.2-19",
@@ -727,6 +882,19 @@
       ],
       "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
     },
+    "dqrng": {
+      "Package": "dqrng",
+      "Version": "0.3.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "BH",
+        "R",
+        "Rcpp",
+        "sitmo"
+      ],
+      "Hash": "a8fa88d5e211585a234c1bbb03e797ae"
+    },
     "dtplyr": {
       "Package": "dtplyr",
       "Version": "1.3.1",
@@ -746,6 +914,22 @@
       ],
       "Hash": "54ed3ea01b11e81a86544faaecfef8e2"
     },
+    "edgeR": {
+      "Package": "edgeR",
+      "Version": "3.42.4",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "R",
+        "Rcpp",
+        "graphics",
+        "limma",
+        "locfit",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "3186512bacaffb43a1f37e6f26d3b72c"
+    },
     "ellipsis": {
       "Package": "ellipsis",
       "Version": "0.3.2",
@@ -1092,6 +1276,41 @@
       ],
       "Hash": "99df65cfef20e525ed38c3d2577f7190"
     },
+    "igraph": {
+      "Package": "igraph",
+      "Version": "1.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "cli",
+        "cpp11",
+        "grDevices",
+        "graphics",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pkgconfig",
+        "rlang",
+        "stats",
+        "utils"
+      ],
+      "Hash": "80401cb5ec513e8ddc56764d03f63669"
+    },
+    "irlba": {
+      "Package": "irlba",
+      "Version": "2.3.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "methods",
+        "stats"
+      ],
+      "Hash": "acb06a47b732c6251afd16e19c3201ff"
+    },
     "isoband": {
       "Package": "isoband",
       "Version": "0.2.7",
@@ -1199,6 +1418,20 @@
       ],
       "Hash": "001cecbeac1cff9301bdc3775ee46a86"
     },
+    "limma": {
+      "Package": "limma",
+      "Version": "3.56.2",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "15b74284b9eb4641fa99a01e445a8256"
+    },
     "locfit": {
       "Package": "locfit",
       "Version": "1.5-9.8",
@@ -1254,6 +1487,15 @@
       ],
       "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
     },
+    "metapod": {
+      "Package": "metapod",
+      "Version": "1.8.0",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "Rcpp"
+      ],
+      "Hash": "577022e3e4c4d3a3c812aefbe640467e"
+    },
     "mgcv": {
       "Package": "mgcv",
       "Version": "1.8-42",
@@ -1583,6 +1825,17 @@
       "Repository": "RSPM",
       "Hash": "5564500e25cffad9e22244ced1379887"
     },
+    "rsvd": {
+      "Package": "rsvd",
+      "Version": "1.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Matrix",
+        "R"
+      ],
+      "Hash": "b462187d887abc519894874486dbd6fd"
+    },
     "rvest": {
       "Package": "rvest",
       "Version": "1.0.3",
@@ -1635,6 +1888,59 @@
       ],
       "Hash": "906cb23d2f1c5680b8ce439b44c6fa63"
     },
+    "scran": {
+      "Package": "scran",
+      "Version": "1.28.2",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BH",
+        "BiocGenerics",
+        "BiocParallel",
+        "BiocSingular",
+        "DelayedArray",
+        "DelayedMatrixStats",
+        "Matrix",
+        "Rcpp",
+        "S4Vectors",
+        "SingleCellExperiment",
+        "SummarizedExperiment",
+        "beachmat",
+        "bluster",
+        "dqrng",
+        "edgeR",
+        "igraph",
+        "limma",
+        "metapod",
+        "methods",
+        "scuttle",
+        "statmod",
+        "stats",
+        "utils"
+      ],
+      "Hash": "ad52c1517a09929ca3ab0a622a22e0a3"
+    },
+    "scuttle": {
+      "Package": "scuttle",
+      "Version": "1.10.2",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "BiocGenerics",
+        "BiocParallel",
+        "DelayedArray",
+        "DelayedMatrixStats",
+        "GenomicRanges",
+        "Matrix",
+        "Rcpp",
+        "S4Vectors",
+        "SingleCellExperiment",
+        "SummarizedExperiment",
+        "beachmat",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "c81a27288455b3d22465df1e9cfc9dc0"
+    },
     "selectr": {
       "Package": "selectr",
       "Version": "0.4-2",
@@ -1648,6 +1954,17 @@
       ],
       "Hash": "3838071b66e0c566d55cc26bd6e27bf4"
     },
+    "sitmo": {
+      "Package": "sitmo",
+      "Version": "2.0.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "Rcpp"
+      ],
+      "Hash": "c956d93f6768a9789edbc13072b70c78"
+    },
     "snow": {
       "Package": "snow",
       "Version": "0.4-4",
@@ -1659,6 +1976,31 @@
       ],
       "Hash": "40b74690debd20c57d93d8c246b305d4"
     },
+    "sparseMatrixStats": {
+      "Package": "sparseMatrixStats",
+      "Version": "1.12.2",
+      "Source": "Bioconductor",
+      "Requirements": [
+        "Matrix",
+        "MatrixGenerics",
+        "Rcpp",
+        "matrixStats",
+        "methods"
+      ],
+      "Hash": "4392d3abdce514b427a1389b7e3d2514"
+    },
+    "statmod": {
+      "Package": "statmod",
+      "Version": "1.5.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "26e158d12052c279bdd4ba858b80fb1f"
+    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.7.12",