Merge remote-tracking branch 'origin/bioconductor-import-branch'

Author: Tools Platform Ecosystem bot

imports/bioconductor/affy.bioconductor.json

@@ -123,7 +123,6 @@
         "puma",
         "pvac",
         "rat2302frmavecs",
-        "seeker",
         "signatureSearchData",
         "tilingArray",
         "vsn"

imports/bioconductor/alabaster.base.bioconductor.json

@@ -46,7 +46,7 @@
         "DataRepresentation",
         "Software"
     ],
-    "dependencyCount": "16",
+    "dependencyCount": "17",
     "dependsOnMe": [
         "alabaster",
         "alabaster.bumpy",

imports/bioconductor/alabaster.bumpy.bioconductor.json

@@ -38,7 +38,7 @@
         "DataRepresentation",
         "Software"
     ],
-    "dependencyCount": "23",
+    "dependencyCount": "24",
     "git_branch": "RELEASE_3_20",
     "git_last_commit": "901aad8",
     "git_last_commit_date": "2024-10-29",

imports/bioconductor/alabaster.matrix.bioconductor.json

@@ -46,7 +46,7 @@
         "DataRepresentation",
         "Software"
     ],
-    "dependencyCount": "33",
+    "dependencyCount": "34",
     "git_branch": "RELEASE_3_20",
     "git_last_commit": "d176a56",
     "git_last_commit_date": "2024-11-19",

imports/bioconductor/annotate.bioconductor.json

@@ -96,7 +96,6 @@
         "categoryCompare",
         "codelink",
         "debrowser",
-        "easyDifferentialGeneCoexpression",
         "geneExpressionFromGEO",
         "genefilter",
         "globaltest",

imports/bioconductor/annotationdbi.bioconductor.json

@@ -941,7 +941,6 @@
         "scTensor",
         "scanMiRApp",
         "scruff",
-        "seeker",
         "signatureSearch",
         "simplifyEnrichment",
         "soybeancdf",

imports/bioconductor/arrayexpress.bioconductor.json

@@ -55,8 +55,7 @@
     "source.ver": "src/contrib/ArrayExpress_1.66.0.tar.gz",
     "suggestsMe": [
         "Hiiragi2013",
-        "bapred",
-        "seeker"
+        "bapred"
     ],
     "vignetteTitles": [
         "ArrayExpress: Import and convert ArrayExpress data sets into R object"

imports/bioconductor/biobase.bioconductor.json

@@ -474,7 +474,6 @@
         "debCAM",
         "destiny",
         "discordant",
-        "easyDifferentialGeneCoexpression",
         "easyRNASeq",
         "ecolitk",
         "ensembldb",
@@ -684,7 +683,6 @@
         "rsconnect",
         "scater",
         "scmeth",
-        "seeker",
         "seventyGeneData",
         "sigminer",
         "sparrow",

imports/bioconductor/biomart.bioconductor.json

@@ -134,7 +134,6 @@
         "rgsepd",
         "scGOclust",
         "scPipe",
-        "seeker",
         "seq2pathway",
         "sitadela",
         "snplinkage",

imports/bioconductor/biomformat.bioconductor.json

@@ -61,6 +61,7 @@
         "MicrobiotaProcess",
         "animalcules",
         "iSEEtree",
+        "metacoder",
         "metagenomeSeq",
         "mia"
     ],