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

Author: Tools Platform Ecosystem bot

imports/bioconductor/aldex2.bioconductor.json

@@ -62,7 +62,7 @@
         "Software",
         "Transcriptomics"
     ],
-    "dependencyCount": "68",
+    "dependencyCount": "67",
     "dependsOnMe": [
         "omicplotR"
     ],
@@ -76,7 +76,8 @@
     "hasREADME": false,
     "importsMe": [
         "aIc",
-        "benchdamic"
+        "benchdamic",
+        "microbiomeMarker"
     ],
     "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/ALDEx2_1.38.0.tgz",
     "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/ALDEx2_1.38.0.tgz",

imports/bioconductor/alpsnmr.bioconductor.json

@@ -82,7 +82,7 @@
         "Software",
         "Visualization"
     ],
-    "dependencyCount": "132",
+    "dependencyCount": "131",
     "git_branch": "RELEASE_3_20",
     "git_last_commit": "ab34115",
     "git_last_commit_date": "2024-10-29",

imports/bioconductor/ancombc.bioconductor.json

@@ -77,7 +77,8 @@
     "hasNEWS": true,
     "hasREADME": false,
     "importsMe": [
-        "benchdamic"
+        "benchdamic",
+        "microbiomeMarker"
     ],
     "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/ANCOMBC_2.8.1.tgz",
     "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/ANCOMBC_2.8.1.tgz",

imports/bioconductor/annotationdbi.bioconductor.json

@@ -1019,6 +1019,7 @@
         "conos",
         "csaw",
         "curatedAdipoChIP",
+        "dnapath",
         "easylabel",
         "edgeR",
         "eisaR",

imports/bioconductor/anvil.bioconductor.citation.html

@@ -1,4 +1,4 @@
 <p>Ramos M, Morgan M, Interdonato K, Cheng Y, Turaga N (2025).
 <em>AnVIL: Bioconductor on the AnVIL compute environment</em>.
-R package version 1.18.4. 
+R package version 1.18.5. 
 </p>

imports/bioconductor/anvil.bioconductor.json

@@ -1,6 +1,6 @@
 {
     "Author": "Marcel Ramos [aut, cre] (<https://orcid.org/0000-0002-3242-0582>), Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>), Kayla Interdonato [aut], Yubo Cheng [aut], Nitesh Turaga [aut], BJ Stubbs [ctb], Vincent Carey [ctb], Sehyun Oh [ctb], Sweta Gopaulakrishnan [ctb], Valerie Obenchain [ctb]",
-    "Date/Publication": "2025-01-27",
+    "Date/Publication": "2025-02-24",
     "Depends": [
         "AnVILBase",
         "R (>= 3.6)",
@@ -28,7 +28,7 @@
         "yaml"
     ],
     "License": "Artistic-2.0",
-    "MD5sum": "3af9eff5d4e8973b0503f917c8921c67",
+    "MD5sum": "c8de64f7c394016c2fe6474347e6c11d",
     "Maintainer": "Marcel Ramos <marcel.ramos@sph.cuny.edu>",
     "NeedsCompilation": "no",
     "Package": "AnVIL",
@@ -52,7 +52,7 @@
         "withr"
     ],
     "Title": "Bioconductor on the AnVIL compute environment",
-    "Version": "1.18.4",
+    "Version": "1.18.5",
     "VignetteBuilder": "knitr",
     "biocViews": [
         "Infrastructure",
@@ -63,8 +63,8 @@
         "cBioPortalData"
     ],
     "git_branch": "RELEASE_3_20",
-    "git_last_commit": "d566998",
-    "git_last_commit_date": "2025-01-24",
+    "git_last_commit": "f97f68c",
+    "git_last_commit_date": "2025-02-24",
     "git_url": "https://git.bioconductor.org/packages/AnVIL",
     "hasINSTALL": false,
     "hasLICENSE": false,
@@ -75,9 +75,9 @@
         "AnVILWorkflow",
         "terraTCGAdata"
     ],
-    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/AnVIL_1.18.4.tgz",
-    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/AnVIL_1.18.4.tgz",
-    "source.ver": "src/contrib/AnVIL_1.18.4.tar.gz",
+    "mac.binary.big-sur-arm64.ver": "bin/macosx/big-sur-arm64/contrib/4.4/AnVIL_1.18.5.tgz",
+    "mac.binary.big-sur-x86_64.ver": "bin/macosx/big-sur-x86_64/contrib/4.4/AnVIL_1.18.5.tgz",
+    "source.ver": "src/contrib/AnVIL_1.18.5.tar.gz",
     "suggestsMe": [
         "AnVILBase",
         "AnVILGCP"
@@ -92,5 +92,5 @@
         "vignettes/AnVIL/inst/doc/Introduction.html",
         "vignettes/AnVIL/inst/doc/RunningWorkflow.html"
     ],
-    "win.binary.ver": "bin/windows/contrib/4.4/AnVIL_1.18.4.zip"
+    "win.binary.ver": "bin/windows/contrib/4.4/AnVIL_1.18.5.zip"
 }

imports/bioconductor/benchdamic.bioconductor.json

@@ -75,7 +75,7 @@
         "Preprocessing",
         "Software"
     ],
-    "dependencyCount": "374",
+    "dependencyCount": "373",
     "git_branch": "RELEASE_3_20",
     "git_last_commit": "ef8ce31",
     "git_last_commit_date": "2024-11-26",

imports/bioconductor/biobase.bioconductor.json

@@ -525,6 +525,7 @@
         "mfa",
         "miRSM",
         "microbiomeDASim",
+        "microbiomeMarker",
         "minfi",
         "missMethyl",
         "mogsa",

imports/bioconductor/biocgenerics.bioconductor.json

@@ -501,6 +501,7 @@
         "mia",
         "miaViz",
         "microbiomeDataSets",
+        "microbiomeMarker",
         "miloR",
         "mimager",
         "missMethyl",

imports/bioconductor/bioconcotk.bioconductor.citation.html

@@ -91,6 +91,19 @@
 
     <header id="site-masthead" class="site-masthead">
   <div class="announcement announcement-brand">
+ <svg xmlns="http://www.w3.org/2000/svg" width="19" height="18" viewBox="0 0 19 18" fill="none">
+     <path
+       d="M9.50003 6.75V8.25M9.50003 11.25H9.50753M4.30387 14.25H14.6962C15.8509 14.25 16.5726 13 15.9952 12L10.7991 3C10.2217 2 8.77834 2 8.20099 3L3.00484 12C2.42749 13 3.14917 14.25 4.30387 14.25Z"
+       stroke-width="1.5" stroke-linecap="round" stroke-linejoin="round" />
+ </svg>
+
+     <p style="font-size:125%">
+     Registration and Abstract Submission Open for
+     <br>
+     <a href="https://gbcc2025.bioconductor.org/">GBCC2025</a>: Joint Galaxy/Bioconductor Conference
+    <br>
+    Early registration discount pricing ends March 31!
+    </p>
 </div>
 
   <!-- If there are no announcements, comment out the element  -->