diff --git a/tools/scater/macros.xml b/tools/scater/macros.xml
index 9ec9f6c0c19..9e8187b29a1 100644
--- a/tools/scater/macros.xml
+++ b/tools/scater/macros.xml
@@ -1,12 +1,12 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.28.0</token>
+    <token name="@TOOL_VERSION@">1.30.1</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-scater</requirement>
             <requirement type="package" version="1.7.3">r-optparse</requirement>
             <requirement type="package" version="0.0.8">r-workflowscriptscommon</requirement>
-            <requirement type="package" version="1.18.0">bioconductor-loomexperiment</requirement>
+            <requirement type="package" version="1.20.0">bioconductor-loomexperiment</requirement>
             <yield />
         </requirements>
     </xml>
diff --git a/tools/scater/scater-plot-dist-scatter.xml b/tools/scater/scater-plot-dist-scatter.xml
index a44be3176cc..2287a6b6c88 100644
--- a/tools/scater/scater-plot-dist-scatter.xml
+++ b/tools/scater/scater-plot-dist-scatter.xml
@@ -6,7 +6,7 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="0.6.0">r-ggpubr</requirement>
-        <requirement type="package" version="1.2.1">r-scales</requirement>
+        <requirement type="package" version="1.3.0">r-scales</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
diff --git a/tools/scater/scater-plot-tsne.xml b/tools/scater/scater-plot-tsne.xml
index 461a03fcdac..d5b70b61d9a 100644
--- a/tools/scater/scater-plot-tsne.xml
+++ b/tools/scater/scater-plot-tsne.xml
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.16">r-rtsne</requirement>
+        <requirement type="package" version="0.17">r-rtsne</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/scater-plot-tsne.R'