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

Author: Tools Platform Ecosystem bot

imports/bioconductor/batchelor.bioconductor.json

@@ -84,6 +84,7 @@
         "SCIntRuler",
         "mumosa",
         "scMerge",
+        "scPipeline",
         "singleCellTK"
     ],
     "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/batchelor_1.22.0.tgz",

imports/bioconductor/biobase.bioconductor.json

@@ -325,7 +325,6 @@
         "ConsensusClusterPlus",
         "CoreGx",
         "CytoML",
-        "D4TAlink.light",
         "DAPAR",
         "DEGreport",
         "DESeq2",

imports/bioconductor/biocgenerics.bioconductor.json

@@ -269,7 +269,6 @@
         "MetaboAnnotation",
         "MethylAid",
         "MiRaGE",
-        "MicroSEC",
         "MinimumDistance",
         "Modstrings",
         "Moonlight2R",
@@ -484,7 +483,6 @@
         "infercnv",
         "intansv",
         "isomiRs",
-        "kmeRs",
         "ldblock",
         "lemur",
         "lisaClust",

imports/bioconductor/biocneighbors.bioconductor.json

@@ -78,6 +78,7 @@
     "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/BiocNeighbors_2.0.1.tgz",
     "source.ver": "src/contrib/BiocNeighbors_2.0.1.tar.gz",
     "suggestsMe": [
+        "ClassifyR",
         "TSCAN",
         "TrajectoryUtils"
     ],

imports/bioconductor/biomart.bioconductor.json

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

imports/bioconductor/biostrings.bioconductor.json

@@ -102,7 +102,6 @@
         "SCAN.UPC",
         "SELEX",
         "SICtools",
-        "STRMPS",
         "ShortRead",
         "SimFFPE",
         "Structstrings",
@@ -387,7 +386,6 @@
         "MatrixRider",
         "MesKit",
         "MetaScope",
-        "MicroSEC",
         "MicrobiotaProcess",
         "MitoHEAR",
         "MixviR",
@@ -502,7 +500,6 @@
         "immuneSIM",
         "ipdDb",
         "kibior",
-        "kmeRs",
         "kmeRtone",
         "longreadvqs",
         "m6Aboost",

imports/bioconductor/bugsigdbr.bioconductor.json

@@ -2,7 +2,7 @@
     "Archs": "x64",
     "Author": "Ludwig Geistlinger [aut, cre], Jennifer Wokaty [aut], Levi Waldron [aut]",
     "BugReports": "https://github.com/waldronlab/bugsigdbr/issues",
-    "Date/Publication": "2025-03-03",
+    "Date/Publication": "2025-03-10",
     "Depends": [
         "R (>= 4.1)"
     ],
@@ -14,7 +14,7 @@
         "vroom"
     ],
     "License": "GPL-3",
-    "MD5sum": "30809a39ef89696ea535af156ad268b0",
+    "MD5sum": "7e72c2a860979be11308877ab586a2f0",
     "Maintainer": "Ludwig Geistlinger <ludwig.geistlinger@gmail.com>",
     "NeedsCompilation": "no",
     "Package": "bugsigdbr",
@@ -31,7 +31,7 @@
     ],
     "Title": "R-side access to published microbial signatures from BugSigDB",
     "URL": "https://github.com/waldronlab/bugsigdbr",
-    "Version": "1.12.1",
+    "Version": "1.12.3",
     "VignetteBuilder": "knitr",
     "biocViews": [
         "DataImport",
@@ -42,21 +42,21 @@
     ],
     "dependencyCount": "52",
     "git_branch": "RELEASE_3_20",
-    "git_last_commit": "d06f976",
-    "git_last_commit_date": "2025-02-28",
+    "git_last_commit": "f49c6da",
+    "git_last_commit_date": "2025-03-07",
     "git_url": "https://git.bioconductor.org/packages/bugsigdbr",
     "hasINSTALL": false,
     "hasLICENSE": false,
     "hasNEWS": true,
     "hasREADME": false,
-    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/bugsigdbr_1.12.1.tgz",
-    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/bugsigdbr_1.12.1.tgz",
-    "source.ver": "src/contrib/bugsigdbr_1.12.1.tar.gz",
+    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/bugsigdbr_1.12.3.tgz",
+    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/bugsigdbr_1.12.3.tgz",
+    "source.ver": "src/contrib/bugsigdbr_1.12.3.tar.gz",
     "vignetteTitles": [
         "R-side access to BugSigDB"
     ],
     "vignettes": [
         "vignettes/bugsigdbr/inst/doc/bugsigdbr.html"
     ],
-    "win.binary.ver": "bin/windows/contrib/4.4/bugsigdbr_1.12.1.zip"
+    "win.binary.ver": "bin/windows/contrib/4.4/bugsigdbr_1.12.3.zip"
 }

imports/bioconductor/classifyr.bioconductor.json

@@ -1,7 +1,7 @@
 {
     "Archs": "x64",
     "Author": "Dario Strbenac [aut, cre], Ellis Patrick [aut], Sourish Iyengar [aut], Harry Robertson [aut], Andy Tran [aut], John Ormerod [aut], Graham Mann [aut], Jean Yang [aut]",
-    "Date/Publication": "2025-02-03",
+    "Date/Publication": "2025-03-10",
     "Depends": [
         "BiocParallel",
         "MultiAssayExperiment",
@@ -28,7 +28,7 @@
         "utils"
     ],
     "License": "GPL-3",
-    "MD5sum": "b6a3be0aca26bd356408787edfe36c4d",
+    "MD5sum": "bd8c0c69c460a0067515bcdc2e969b30",
     "Maintainer": "Dario Strbenac <dario.strbenac@sydney.edu.au>",
     "NeedsCompilation": "yes",
     "Package": "ClassifyR",
@@ -38,11 +38,13 @@
         "vignettes/ClassifyR/inst/doc/DevelopersGuide.R"
     ],
     "Suggests": [
+        "BiocNeighbors",
         "BiocStyle",
         "IRanges",
         "MatrixModels",
         "PoiClaClu",
         "Rmixmod",
+        "TOP",
         "car",
         "class",
         "cowplot",
@@ -65,7 +67,7 @@
     ],
     "Title": "A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing",
     "URL": "https://sydneybiox.github.io/ClassifyR/",
-    "Version": "3.10.6",
+    "Version": "3.10.9",
     "VignetteBuilder": "knitr",
     "biocViews": [
         "Classification",
@@ -74,8 +76,8 @@
     ],
     "dependencyCount": "146",
     "git_branch": "RELEASE_3_20",
-    "git_last_commit": "b501969",
-    "git_last_commit_date": "2025-01-30",
+    "git_last_commit": "184aecd",
+    "git_last_commit_date": "2025-03-09",
     "git_url": "https://git.bioconductor.org/packages/ClassifyR",
     "hasINSTALL": false,
     "hasLICENSE": false,
@@ -85,9 +87,9 @@
         "TOP",
         "spicyR"
     ],
-    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/ClassifyR_3.10.6.tgz",
-    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/ClassifyR_3.10.6.tgz",
-    "source.ver": "src/contrib/ClassifyR_3.10.6.tar.gz",
+    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/ClassifyR_3.10.9.tgz",
+    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/ClassifyR_3.10.9.tgz",
+    "source.ver": "src/contrib/ClassifyR_3.10.9.tar.gz",
     "suggestsMe": [
         "Statial",
         "scFeatures",
@@ -101,5 +103,5 @@
         "vignettes/ClassifyR/inst/doc/ClassifyR.html",
         "vignettes/ClassifyR/inst/doc/DevelopersGuide.html"
     ],
-    "win.binary.ver": "bin/windows/contrib/4.4/ClassifyR_3.10.6.zip"
+    "win.binary.ver": "bin/windows/contrib/4.4/ClassifyR_3.10.9.zip"
 }

imports/bioconductor/complexheatmap.bioconductor.json

@@ -131,6 +131,7 @@
         "RNAseqQC",
         "RVA",
         "SPONGE",
+        "SeuratExplorer",
         "TCGAWorkflow",
         "TMSig",
         "TransProR",

imports/bioconductor/crlmm.bioconductor.json

@@ -1,6 +1,6 @@
 {
     "Author": "Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry",
-    "Date/Publication": "2024-10-29",
+    "Date/Publication": "2025-03-06",
     "Depends": [
         "R (>= 2.14.0)",
         "oligoClasses (>= 1.21.12)",
@@ -33,7 +33,7 @@
     "LinkingTo": [
         "preprocessCore (>= 1.17.7)"
     ],
-    "MD5sum": "1f4e6f2c08d05240cb5ccb9165247de5",
+    "MD5sum": "66dc28572aeb79299641f5d9047079c8",
     "Maintainer": "Benilton S Carvalho <benilton@unicamp.br>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>",
     "NeedsCompilation": "yes",
     "Package": "crlmm",
@@ -48,7 +48,7 @@
         "snpStats"
     ],
     "Title": "Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays",
-    "Version": "1.64.0",
+    "Version": "1.64.1",
     "biocViews": [
         "CopyNumberVariation",
         "Microarray",
@@ -61,8 +61,8 @@
         "MAGAR"
     ],
     "git_branch": "RELEASE_3_20",
-    "git_last_commit": "f1bd3c9",
-    "git_last_commit_date": "2024-10-29",
+    "git_last_commit": "bb00538",
+    "git_last_commit_date": "2025-03-04",
     "git_url": "https://git.bioconductor.org/packages/crlmm",
     "hasINSTALL": false,
     "hasLICENSE": false,
@@ -71,9 +71,9 @@
     "importsMe": [
         "VanillaICE"
     ],
-    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/crlmm_1.64.0.tgz",
-    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/crlmm_1.64.0.tgz",
-    "source.ver": "src/contrib/crlmm_1.64.0.tar.gz",
+    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/crlmm_1.64.1.tgz",
+    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/crlmm_1.64.1.tgz",
+    "source.ver": "src/contrib/crlmm_1.64.1.tar.gz",
     "suggestsMe": [
         "hapmap370k",
         "oligoClasses"
@@ -94,5 +94,5 @@
         "vignettes/crlmm/inst/doc/genotyping.pdf",
         "vignettes/crlmm/inst/doc/gtypeDownstream.pdf"
     ],
-    "win.binary.ver": "bin/windows/contrib/4.4/crlmm_1.64.0.zip"
+    "win.binary.ver": "bin/windows/contrib/4.4/crlmm_1.64.1.zip"
 }