diff --git a/.release-please-manifest.json b/.release-please-manifest.json
index e6f877563b..411256bcab 100644
--- a/.release-please-manifest.json
+++ b/.release-please-manifest.json
@@ -1,3 +1,3 @@
 {
-  ".": "4.0.0"
+  ".": "4.1.0"
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8daf7c113..14790b0ae7 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,35 @@
 * --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)
 
+## [4.1.0](https://github.com/deeptools/deepTools/compare/4.0.0...4.1.0) (2026-09-23)
+
+
+### Features
+
+* deprecate *_old entrypoints ([#1473](https://github.com/deeptools/deepTools/issues/1473)) ([dfbf3e6](https://github.com/deeptools/deepTools/commit/dfbf3e6483ce0440003e51751b6fd37ce13339c5))
+* deprecate compute/correctGCbias ([#1471](https://github.com/deeptools/deepTools/issues/1471)) ([ec4fbc8](https://github.com/deeptools/deepTools/commit/ec4fbc8018434f2cf04353d3b58116f09175de00))
+* exit if provided number of labels doesn't match number of samples (closes [#1026](https://github.com/deeptools/deepTools/issues/1026)) ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* explicit check for start < end in bed ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* PCA drop --transpose/--centerRows as scores are default now in plotPCA ([#1472](https://github.com/deeptools/deepTools/issues/1472)) ([0604617](https://github.com/deeptools/deepTools/commit/060461736e573252f2d00099481086a0279ce7e1))
+* script for ESS calculation ([#1474](https://github.com/deeptools/deepTools/issues/1474)) ([cde2aa7](https://github.com/deeptools/deepTools/commit/cde2aa7938cb4af6fe28de1504f94f6928344342))
+
+
+### Bug Fixes
+
+* do not allow RPGC in bamCompare mode anymore (closes [#1404](https://github.com/deeptools/deepTools/issues/1404)) ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* remove np.warnings, keep ignores in the function context instead of propagating to end of function/tool ([#1478](https://github.com/deeptools/deepTools/issues/1478)) ([2aab71a](https://github.com/deeptools/deepTools/commit/2aab71a49875ae43b05f6d508432730714e99bb9))
+
+
+### Documentation
+
+* fix visual shift under - strand for alSieve documentation (closes [#1331](https://github.com/deeptools/deepTools/issues/1331)) ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* include release DOI in README ([0604617](https://github.com/deeptools/deepTools/commit/060461736e573252f2d00099481086a0279ce7e1))
+* make contribution.md a bit more verbose ([0604617](https://github.com/deeptools/deepTools/commit/060461736e573252f2d00099481086a0279ce7e1))
+* 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))
+* more verbose help on filterRNAstrand (closes [#1248](https://github.com/deeptools/deepTools/issues/1248)) ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* normalizeUsing in parserCommon has None explained first (closes [#1311](https://github.com/deeptools/deepTools/issues/1311)) ([b0a2841](https://github.com/deeptools/deepTools/commit/b0a28418afe6a6b76bff17cf580a41bc607090c5))
+* update ess for latest assemblies in listed table ([cde2aa7](https://github.com/deeptools/deepTools/commit/cde2aa7938cb4af6fe28de1504f94f6928344342))
+
 ## 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 618ee2dde4..f3c4d1e1cc 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@">4.1.0</token> <!-- x-release-please-version -->
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@GALAXY_VERSION@">23.2</token>
     <xml name="requirements">
diff --git a/pyproject.toml b/pyproject.toml
index ded513f661..91d9561e9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ bindings = "pyo3"
 
 [project]
 name = "deeptools"
-version = "4.0.0"
+version = "4.1.0"
 authors = [
     {name="Vivek Bhardwaj"},
     {name="Ward Deboutte"},