diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml
index 3e9cc201b770..445fed3ca21b 100644
--- a/modules/nf-core/shinyngs/app/environment.yml
+++ b/modules/nf-core/shinyngs/app/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.4
+  - bioconda::r-shinyngs=2.3.0
diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
index 2e956ad6c2bc..65b32f819f66 100644
--- a/modules/nf-core/shinyngs/app/main.nf
+++ b/modules/nf-core/shinyngs/app/main.nf
@@ -14,8 +14,8 @@ process SHINYNGS_APP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fc080dc45831489dd70b8183314a5a6f840064d6c78f3466790df0fba1503d0/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.4--2bf759f8be585e75' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)    // Experiment-level info
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
index ba39909e29b1..c7d75089a22d 100644
--- a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
@@ -4,41 +4,41 @@
             "data.rds",
             "app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
             [
-                "versions.yml:md5,a7165231603c3f0675568989e1c16c36"
+                "versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:42:06.649371488"
+        "timestamp": "2025-12-01T17:45:00.111194977"
     },
     "mouse - multi matrix": {
         "content": [
             "data.rds",
             "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
             [
-                "versions.yml:md5,a7165231603c3f0675568989e1c16c36"
+                "versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:41:14.463468708"
+        "timestamp": "2025-12-01T17:44:28.229851192"
     },
     "mouse - single matrix": {
         "content": [
             "data.rds",
             "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
             [
-                "versions.yml:md5,a7165231603c3f0675568989e1c16c36"
+                "versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:41:43.718285268"
+        "timestamp": "2025-12-01T17:44:47.274942197"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml
index 3e9cc201b770..445fed3ca21b 100644
--- a/modules/nf-core/shinyngs/staticdifferential/environment.yml
+++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.4
+  - bioconda::r-shinyngs=2.3.0
diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
index 06f040ba1f26..44995ea4296a 100644
--- a/modules/nf-core/shinyngs/staticdifferential/main.nf
+++ b/modules/nf-core/shinyngs/staticdifferential/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fc080dc45831489dd70b8183314a5a6f840064d6c78f3466790df0fba1503d0/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.4--2bf759f8be585e75' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
 
     input:
     tuple val(meta), path(differential_result)                              // Differential info: contrast and differential stats
diff --git a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
index fc72a836471e..22d2c20edb21 100644
--- a/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                 
             ],
             [
-                "versions.yml:md5,b354e83a028f5c38cf61821a927a92d7"
+                "versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:42:43.682019774"
+        "timestamp": "2025-12-01T17:45:23.17214359"
     },
     "stub": {
         "content": [
@@ -43,10 +43,10 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b354e83a028f5c38cf61821a927a92d7"
+                    "versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
                 ],
                 "versions": [
-                    "versions.yml:md5,b354e83a028f5c38cf61821a927a92d7"
+                    "versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
                 ],
                 "volcanos_html": [
                     [
@@ -75,9 +75,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:43:05.46187287"
+        "timestamp": "2025-12-01T17:45:36.887175944"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml
index 3e9cc201b770..445fed3ca21b 100644
--- a/modules/nf-core/shinyngs/staticexploratory/environment.yml
+++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.4
+  - bioconda::r-shinyngs=2.3.0
diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
index 7cc096ae7c04..6819d05afd63 100644
--- a/modules/nf-core/shinyngs/staticexploratory/main.nf
+++ b/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICEXPLORATORY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fc080dc45831489dd70b8183314a5a6f840064d6c78f3466790df0fba1503d0/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.4--2bf759f8be585e75' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files), val(variable)
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
index db0426babf6c..4f11d0f72470 100644
--- a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
@@ -8,14 +8,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,ccb51082df7cfed8fad43e1bbaf6dc63"
+                "versions.yml:md5,91989cb95f99f7921bf93946d2e9131c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:37:50.314588599"
+        "timestamp": "2025-12-01T17:46:11.289150469"
     },
     "mouse - defaults": {
         "content": [
@@ -26,14 +26,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,ccb51082df7cfed8fad43e1bbaf6dc63"
+                "versions.yml:md5,91989cb95f99f7921bf93946d2e9131c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:37:32.399343012"
+        "timestamp": "2025-12-01T17:45:58.516740998"
     },
     "mouse - specify log": {
         "content": [
@@ -44,14 +44,14 @@
             "pca3d.png",
             "sample_dendrogram.png",
             [
-                "versions.yml:md5,ccb51082df7cfed8fad43e1bbaf6dc63"
+                "versions.yml:md5,91989cb95f99f7921bf93946d2e9131c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:38:16.545811656"
+        "timestamp": "2025-12-01T17:46:32.257225071"
     },
     "mouse - html": {
         "content": [
@@ -67,13 +67,13 @@
             false,
             false,
             [
-                "versions.yml:md5,ccb51082df7cfed8fad43e1bbaf6dc63"
+                "versions.yml:md5,91989cb95f99f7921bf93946d2e9131c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:38:44.838937428"
+        "timestamp": "2025-12-01T17:46:55.235470561"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
index 3e9cc201b770..445fed3ca21b 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
+++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::r-shinyngs=2.2.4
+  - bioconda::r-shinyngs=2.3.0
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
index 78990f53cbda..fed28dc96fa8 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf
+++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fc080dc45831489dd70b8183314a5a6f840064d6c78f3466790df0fba1503d0/data' :
-        'community.wave.seqera.io/library/r-shinyngs:2.2.4--2bf759f8be585e75' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
+        'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
 
     input:
     tuple val(meta),  path(sample), path(assay_files)
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
index a3ba5f19bf53..3ca81fb269c2 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
+++ b/modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ],
                 "assays": [
                     [
@@ -70,15 +70,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:34:37.174853667"
+        "timestamp": "2025-12-01T17:47:16.763658341"
     },
     "stub": {
         "content": [
@@ -116,7 +116,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ],
                 "assays": [
                     [
@@ -151,15 +151,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:35:23.600562533"
+        "timestamp": "2025-12-01T17:47:52.072518885"
     },
     "test_yaml": {
         "content": [
@@ -197,7 +197,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ],
                 "assays": [
                     [
@@ -232,14 +232,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,07717fd9910caccc6b6606da92af59e6"
+                    "versions.yml:md5,27b6e705643da7c923f338abb7e84dbb"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-02T16:35:04.455614097"
+        "timestamp": "2025-12-01T17:47:38.315342815"
     }
 }
\ No newline at end of file