diff --git a/seurat.yml b/environment.yml
similarity index 100%
rename from seurat.yml
rename to environment.yml
diff --git a/renv.lock b/renv.lock
index e82c48f064444b415d50a2ca3c0f7effa0c7ec18..4817785502bcf1dca6a796ac6bc5997e59a55ffb 100644
--- a/renv.lock
+++ b/renv.lock
@@ -29,9 +29,7 @@
"git_last_commit": "3b2dd91",
"git_last_commit_date": "2022-04-26",
"Hash": "b58c1eb25be406d1a35dd4cff0e9ba2e",
- "Requirements": [
- "BiocGenerics"
- ]
+ "Requirements": []
},
"BiocGenerics": {
"Package": "BiocGenerics",
@@ -72,13 +70,7 @@
"git_last_commit": "4a5afd1",
"git_last_commit_date": "2022-04-26",
"Hash": "c83a6e282a9669d4e04eb2d2ce8660a8",
- "Requirements": [
- "BiocGenerics",
- "IRanges",
- "Matrix",
- "MatrixGenerics",
- "S4Vectors"
- ]
+ "Requirements": []
},
"DelayedMatrixStats": {
"Package": "DelayedMatrixStats",
@@ -89,15 +81,7 @@
"git_last_commit": "50c9aab",
"git_last_commit_date": "2022-04-26",
"Hash": "2d4a83550bedc8a56cc43f4327102f46",
- "Requirements": [
- "DelayedArray",
- "IRanges",
- "Matrix",
- "MatrixGenerics",
- "S4Vectors",
- "matrixStats",
- "sparseMatrixStats"
- ]
+ "Requirements": []
},
"FNN": {
"Package": "FNN",
@@ -116,13 +100,7 @@
"git_last_commit": "69df6a5",
"git_last_commit_date": "2022-09-06",
"Hash": "45eeade5241cbc976f2114f62b90d81d",
- "Requirements": [
- "BiocGenerics",
- "GenomeInfoDbData",
- "IRanges",
- "RCurl",
- "S4Vectors"
- ]
+ "Requirements": []
},
"GenomeInfoDbData": {
"Package": "GenomeInfoDbData",
@@ -140,13 +118,7 @@
"git_last_commit": "2bce608",
"git_last_commit_date": "2022-04-26",
"Hash": "07625db342974bca20a6d82dfc34386d",
- "Requirements": [
- "BiocGenerics",
- "GenomeInfoDb",
- "IRanges",
- "S4Vectors",
- "XVector"
- ]
+ "Requirements": []
},
"HDF5Array": {
"Package": "HDF5Array",
@@ -157,16 +129,7 @@
"git_last_commit": "fb213ba",
"git_last_commit_date": "2022-08-01",
"Hash": "13693baafc480c1bb4005fe6f5e4172f",
- "Requirements": [
- "BiocGenerics",
- "DelayedArray",
- "IRanges",
- "Matrix",
- "Rhdf5lib",
- "S4Vectors",
- "rhdf5",
- "rhdf5filters"
- ]
+ "Requirements": []
},
"IRanges": {
"Package": "IRanges",
@@ -177,10 +140,7 @@
"git_last_commit": "ead506a",
"git_last_commit_date": "2022-08-17",
"Hash": "98cde49c4d8c69377a05cf9a81053254",
- "Requirements": [
- "BiocGenerics",
- "S4Vectors"
- ]
+ "Requirements": []
},
"KernSmooth": {
"Package": "KernSmooth",
@@ -204,9 +164,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "539dc0c0c05636812f1080f473d2c177",
- "Requirements": [
- "lattice"
- ]
+ "Requirements": []
},
"MatrixGenerics": {
"Package": "MatrixGenerics",
@@ -217,9 +175,7 @@
"git_last_commit": "a4a2108",
"git_last_commit_date": "2022-06-23",
"Hash": "0b6a466982071e55981cf5dd8d1c3ceb",
- "Requirements": [
- "matrixStats"
- ]
+ "Requirements": []
},
"R6": {
"Package": "R6",
@@ -251,9 +207,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "19448e3b7f646a99d42660dc025e8f8c",
- "Requirements": [
- "bitops"
- ]
+ "Requirements": []
},
"ROCR": {
"Package": "ROCR",
@@ -261,9 +215,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "cc151930e20e16427bc3d0daec62b4a9",
- "Requirements": [
- "gplots"
- ]
+ "Requirements": []
},
"Rcpp": {
"Package": "Rcpp",
@@ -279,9 +231,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5681153e3eb103725e35ac5f7ebca910",
- "Requirements": [
- "Rcpp"
- ]
+ "Requirements": []
},
"RcppArmadillo": {
"Package": "RcppArmadillo",
@@ -289,9 +239,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "796805fe55a25e42b5e0aeefacc041dc",
- "Requirements": [
- "Rcpp"
- ]
+ "Requirements": []
},
"RcppEigen": {
"Package": "RcppEigen",
@@ -299,10 +247,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4c86baed78388ceb06f88e3e9a1d87f5",
- "Requirements": [
- "Matrix",
- "Rcpp"
- ]
+ "Requirements": []
},
"RcppProgress": {
"Package": "RcppProgress",
@@ -318,9 +263,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f8a578aa91321ecec1292f1e2ffadeda",
- "Requirements": [
- "Rcpp"
- ]
+ "Requirements": []
},
"Rhdf5lib": {
"Package": "Rhdf5lib",
@@ -339,9 +282,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e921b89ef921905fc89b95886675706d",
- "Requirements": [
- "Rcpp"
- ]
+ "Requirements": []
},
"S4Vectors": {
"Package": "S4Vectors",
@@ -352,9 +293,7 @@
"git_last_commit": "f590de3",
"git_last_commit_date": "2022-04-26",
"Hash": "90677cc888563927cecacd4067ccad45",
- "Requirements": [
- "BiocGenerics"
- ]
+ "Requirements": []
},
"Seurat": {
"Package": "Seurat",
@@ -362,51 +301,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0d7350ea71e070760974a50692596c4d",
- "Requirements": [
- "KernSmooth",
- "MASS",
- "Matrix",
- "RANN",
- "RColorBrewer",
- "ROCR",
- "Rcpp",
- "RcppAnnoy",
- "RcppEigen",
- "RcppProgress",
- "Rtsne",
- "SeuratObject",
- "cluster",
- "cowplot",
- "fitdistrplus",
- "future",
- "future.apply",
- "ggplot2",
- "ggrepel",
- "ggridges",
- "httr",
- "ica",
- "igraph",
- "irlba",
- "jsonlite",
- "leiden",
- "lmtest",
- "matrixStats",
- "miniUI",
- "patchwork",
- "pbapply",
- "plotly",
- "png",
- "reticulate",
- "rlang",
- "scales",
- "scattermore",
- "sctransform",
- "shiny",
- "spatstat.core",
- "spatstat.geom",
- "tibble",
- "uwot"
- ]
+ "Requirements": []
},
"SeuratDisk": {
"Package": "SeuratDisk",
@@ -420,18 +315,7 @@
"RemoteRef": "HEAD",
"RemoteSha": "9b89970eac2a3bd770e744f63c7763419486b14c",
"Hash": "18d5d212bad69ae88d2e531c4edb496a",
- "Requirements": [
- "Matrix",
- "R6",
- "Seurat",
- "SeuratObject",
- "cli",
- "crayon",
- "hdf5r",
- "rlang",
- "stringi",
- "withr"
- ]
+ "Requirements": []
},
"SeuratObject": {
"Package": "SeuratObject",
@@ -439,17 +323,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5cfa2058fd095a2d241cf7973cc09d5c",
- "Requirements": [
- "Matrix",
- "Rcpp",
- "RcppEigen",
- "future",
- "future.apply",
- "progressr",
- "rgeos",
- "rlang",
- "sp"
- ]
+ "Requirements": []
},
"SummarizedExperiment": {
"Package": "SummarizedExperiment",
@@ -460,17 +334,7 @@
"git_last_commit": "c8cbd3b",
"git_last_commit_date": "2022-04-28",
"Hash": "7cbcf1fe7236f18f1a961877fbf2d78c",
- "Requirements": [
- "Biobase",
- "BiocGenerics",
- "DelayedArray",
- "GenomeInfoDb",
- "GenomicRanges",
- "IRanges",
- "Matrix",
- "MatrixGenerics",
- "S4Vectors"
- ]
+ "Requirements": []
},
"XVector": {
"Package": "XVector",
@@ -481,12 +345,7 @@
"git_last_commit": "ff6f818",
"git_last_commit_date": "2022-04-26",
"Hash": "03b87ac645463f29d04c2461d5de9610",
- "Requirements": [
- "BiocGenerics",
- "IRanges",
- "S4Vectors",
- "zlibbioc"
- ]
+ "Requirements": []
},
"abind": {
"Package": "abind",
@@ -502,11 +361,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "894108412a7ec23d5de85cdcce871c8b",
- "Requirements": [
- "Rcpp",
- "lattice",
- "nlme"
- ]
+ "Requirements": []
},
"askpass": {
"Package": "askpass",
@@ -514,9 +369,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e8a22846fff485f0be3770c2da758713",
- "Requirements": [
- "sys"
- ]
+ "Requirements": []
},
"backports": {
"Package": "backports",
@@ -543,12 +396,7 @@
"git_last_commit": "3e6af14",
"git_last_commit_date": "2022-04-26",
"Hash": "2a52023b7b17fb9600abe3243b796470",
- "Requirements": [
- "BiocGenerics",
- "DelayedArray",
- "Matrix",
- "Rcpp"
- ]
+ "Requirements": []
},
"bit": {
"Package": "bit",
@@ -564,9 +412,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9fe98599ca456d6552421db0d6772d8f",
- "Requirements": [
- "bit"
- ]
+ "Requirements": []
},
"bitops": {
"Package": "bitops",
@@ -590,15 +436,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "be5ee090716ce1671be6cd5d7c34d091",
- "Requirements": [
- "cachem",
- "htmltools",
- "jquerylib",
- "jsonlite",
- "memoise",
- "rlang",
- "sass"
- ]
+ "Requirements": []
},
"caTools": {
"Package": "caTools",
@@ -606,9 +444,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "34d90fa5845004236b9eacafc51d07b2",
- "Requirements": [
- "bitops"
- ]
+ "Requirements": []
},
"cachem": {
"Package": "cachem",
@@ -616,10 +452,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "648c5b3d71e6a37e3043617489a0a0e9",
- "Requirements": [
- "fastmap",
- "rlang"
- ]
+ "Requirements": []
},
"cellranger": {
"Package": "cellranger",
@@ -627,10 +460,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f61dbaec772ccd2e17705c1e872e9e7c",
- "Requirements": [
- "rematch",
- "tibble"
- ]
+ "Requirements": []
},
"checkmate": {
"Package": "checkmate",
@@ -638,9 +468,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "147e4db6909d8814bb30f671b49d7e06",
- "Requirements": [
- "backports"
- ]
+ "Requirements": []
},
"class": {
"Package": "class",
@@ -648,9 +476,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "da09d82223e669d270e47ed24ac8686e",
- "Requirements": [
- "MASS"
- ]
+ "Requirements": []
},
"cli": {
"Package": "cli",
@@ -674,17 +500,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "79c4a3d0ba7150fb53be125a0708e115",
- "Requirements": [
- "checkmate",
- "dplyr",
- "ggplot2",
- "ggraph",
- "ggrepel",
- "igraph",
- "rlang",
- "tidygraph",
- "viridis"
- ]
+ "Requirements": []
},
"codetools": {
"Package": "codetools",
@@ -716,12 +532,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b418e8423699d11c7f2087c2bfd07da2",
- "Requirements": [
- "ggplot2",
- "gtable",
- "rlang",
- "scales"
- ]
+ "Requirements": []
},
"cpp11": {
"Package": "cpp11",
@@ -745,12 +556,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6aa54f69598c32177e920eb3402e8293",
- "Requirements": [
- "R6",
- "htmltools",
- "jsonlite",
- "lazyeval"
- ]
+ "Requirements": []
},
"curl": {
"Package": "curl",
@@ -798,18 +604,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "539412282059f7f0c07295723d23f987",
- "Requirements": [
- "R6",
- "generics",
- "glue",
- "lifecycle",
- "magrittr",
- "pillar",
- "rlang",
- "tibble",
- "tidyselect",
- "vctrs"
- ]
+ "Requirements": []
},
"dqrng": {
"Package": "dqrng",
@@ -817,11 +612,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "3ce2af5ead3b01c518fd453c7fe5a51a",
- "Requirements": [
- "BH",
- "Rcpp",
- "sitmo"
- ]
+ "Requirements": []
},
"ellipsis": {
"Package": "ellipsis",
@@ -829,9 +620,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077",
- "Requirements": [
- "rlang"
- ]
+ "Requirements": []
},
"fansi": {
"Package": "fansi",
@@ -863,10 +652,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9de7bf56c16871adf44dc88a24c7836c",
- "Requirements": [
- "MASS",
- "survival"
- ]
+ "Requirements": []
},
"fontawesome": {
"Package": "fontawesome",
@@ -874,10 +660,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a36c4a3eade472039a3ec8cb824e6dc4",
- "Requirements": [
- "htmltools",
- "rlang"
- ]
+ "Requirements": []
},
"foreign": {
"Package": "foreign",
@@ -901,12 +684,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f3e26a942d4ee32cec9403e1ddd7000b",
- "Requirements": [
- "digest",
- "globals",
- "listenv",
- "parallelly"
- ]
+ "Requirements": []
},
"future.apply": {
"Package": "future.apply",
@@ -914,10 +692,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "77dbef5c63aa92d1c319ad3b6c10eccb",
- "Requirements": [
- "future",
- "globals"
- ]
+ "Requirements": []
},
"generics": {
"Package": "generics",
@@ -933,20 +708,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5a4414f47b4f9079397d7ebfa46e346b",
- "Requirements": [
- "MASS",
- "Rcpp",
- "RcppEigen",
- "ggplot2",
- "gtable",
- "lifecycle",
- "polyclip",
- "rlang",
- "scales",
- "tidyselect",
- "tweenr",
- "withr"
- ]
+ "Requirements": []
},
"ggplot2": {
"Package": "ggplot2",
@@ -954,18 +716,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0fb26d0674c82705c6b701d1a61e02ea",
- "Requirements": [
- "MASS",
- "digest",
- "glue",
- "gtable",
- "isoband",
- "mgcv",
- "rlang",
- "scales",
- "tibble",
- "withr"
- ]
+ "Requirements": []
},
"ggraph": {
"Package": "ggraph",
@@ -973,23 +724,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "1a60ad958140766d3022ed307474497a",
- "Requirements": [
- "MASS",
- "Rcpp",
- "digest",
- "dplyr",
- "ggforce",
- "ggplot2",
- "ggrepel",
- "graphlayouts",
- "gtable",
- "igraph",
- "rlang",
- "scales",
- "tidygraph",
- "viridis",
- "withr"
- ]
+ "Requirements": []
},
"ggrepel": {
"Package": "ggrepel",
@@ -997,12 +732,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08ab869f37e6a7741a64ab9069bcb67d",
- "Requirements": [
- "Rcpp",
- "ggplot2",
- "rlang",
- "scales"
- ]
+ "Requirements": []
},
"ggridges": {
"Package": "ggridges",
@@ -1010,12 +740,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9d028e8f37c84dba356ce3c367a1978e",
- "Requirements": [
- "ggplot2",
- "plyr",
- "scales",
- "withr"
- ]
+ "Requirements": []
},
"glmGamPoi": {
"Package": "glmGamPoi",
@@ -1026,17 +751,7 @@
"git_last_commit": "b723d61",
"git_last_commit_date": "2022-04-26",
"Hash": "06b4426197431f8bfc48aa68596c69ee",
- "Requirements": [
- "BiocGenerics",
- "DelayedArray",
- "DelayedMatrixStats",
- "HDF5Array",
- "Rcpp",
- "RcppArmadillo",
- "SummarizedExperiment",
- "beachmat",
- "matrixStats"
- ]
+ "Requirements": []
},
"globals": {
"Package": "globals",
@@ -1044,9 +759,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e14798793892c6bebdbe2f144aacf6e6",
- "Requirements": [
- "codetools"
- ]
+ "Requirements": []
},
"glue": {
"Package": "glue",
@@ -1070,11 +783,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "75437dd4c43599f6e9418ea249495fda",
- "Requirements": [
- "KernSmooth",
- "caTools",
- "gtools"
- ]
+ "Requirements": []
},
"graphlayouts": {
"Package": "graphlayouts",
@@ -1082,11 +791,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "33ac314361912f046c6be2556f45921d",
- "Requirements": [
- "Rcpp",
- "RcppArmadillo",
- "igraph"
- ]
+ "Requirements": []
},
"gridExtra": {
"Package": "gridExtra",
@@ -1094,9 +799,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7d7f283939f563670a697165b2cf5560",
- "Requirements": [
- "gtable"
- ]
+ "Requirements": []
},
"gtable": {
"Package": "gtable",
@@ -1120,10 +823,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "73a71a0fd5c0454014ab1b0cd13538f9",
- "Requirements": [
- "R6",
- "bit64"
- ]
+ "Requirements": []
},
"here": {
"Package": "here",
@@ -1131,9 +831,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "24b224366f9c2e7534d2344d10d59211",
- "Requirements": [
- "rprojroot"
- ]
+ "Requirements": []
},
"hms": {
"Package": "hms",
@@ -1141,13 +839,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "41100392191e1244b887878b533eea91",
- "Requirements": [
- "ellipsis",
- "lifecycle",
- "pkgconfig",
- "rlang",
- "vctrs"
- ]
+ "Requirements": []
},
"htmltools": {
"Package": "htmltools",
@@ -1155,12 +847,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6496090a9e00f8354b811d1a2d47b566",
- "Requirements": [
- "base64enc",
- "digest",
- "fastmap",
- "rlang"
- ]
+ "Requirements": []
},
"htmlwidgets": {
"Package": "htmlwidgets",
@@ -1168,11 +855,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "76147821cd3fcd8c4b04e1ef0498e7fb",
- "Requirements": [
- "htmltools",
- "jsonlite",
- "yaml"
- ]
+ "Requirements": []
},
"httpuv": {
"Package": "httpuv",
@@ -1180,12 +863,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fd090e236ae2dc0f0cdf33a9ec83afb6",
- "Requirements": [
- "R6",
- "Rcpp",
- "later",
- "promises"
- ]
+ "Requirements": []
},
"httr": {
"Package": "httr",
@@ -1193,13 +871,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "57557fac46471f0dbbf44705cc6a5c8c",
- "Requirements": [
- "R6",
- "curl",
- "jsonlite",
- "mime",
- "openssl"
- ]
+ "Requirements": []
},
"ica": {
"Package": "ica",
@@ -1215,12 +887,7 @@
"Source": "Repository",
"Repository": "CRAN",
"Hash": "40e38ff98f90967805831b6234afd05f",
- "Requirements": [
- "Matrix",
- "magrittr",
- "pkgconfig",
- "rlang"
- ]
+ "Requirements": []
},
"import": {
"Package": "import",
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@@ -1358,9 +999,7 @@
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@@ -2057,9 +1496,7 @@
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