diff --git a/.release-please-manifest.json b/.release-please-manifest.json
index e6f877563b..cf533f2806 100644
--- a/.release-please-manifest.json
+++ b/.release-please-manifest.json
@@ -1,3 +1,3 @@
 {
-  ".": "4.0.0"
+  ".": "4.0.1"
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8daf7c113..bd48f2738f 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,13 @@
 * --missingDataAsZero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins
 * large scale values precision slightly altered with new backend (f32 vs f64)
 
+## [4.0.1](https://github.com/deeptools/deepTools/compare/4.0.0...4.0.1) (2026-09-16)
+
+
+### Documentation
+
+* make sure changelog in docs reflects changelog in repo ([#1469](https://github.com/deeptools/deepTools/issues/1469)) ([51e50dd](https://github.com/deeptools/deepTools/commit/51e50dd0543a84392ebec09ac090f95da56577fc))
+
 ## 3.5.6
 * minimal supported python version raised to 3.9 (numpy >= 2 support); NaN handling switched to np.nan
 * drop conda usage in pypi/test/planemo CI in favor of pip installs; samtools now pulled from conda-forge/bioconda where still needed in CI
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 1e2b9c13b5..ace6fff412 100755
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -1,7 +1,7 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@TOOL_VERSION@">4.0.0</token> <!-- x-release-please-version -->
+    <token name="@TOOL_VERSION@">4.0.1</token> <!-- x-release-please-version -->
     <token name="@GALAXY_VERSION@">23.2</token>
     <xml name="requirements">
         <requirements>
diff --git a/pyproject.toml b/pyproject.toml
index c3b1438cda..c8d07b3d0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ bindings = "pyo3"
 
 [project]
 name = "deeptools"
-version = "4.0.0"
+version = "4.0.1"
 authors = [
     {name="Vivek Bhardwaj"},
     {name="Ward Deboutte"},