diff --git a/docs/conf.py b/docs/conf.py
index e8f62a607f..4e6861b4da 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -46,7 +46,8 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.autosummary',
-    'sphinxarg.ext'
+    'sphinxarg.ext',
+    'myst_parser'
 ]
 #    'numpydoc'
 
@@ -59,9 +60,10 @@
 templates_path = ['source/_templates']
 
 # The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
diff --git a/docs/content/changelog.md b/docs/content/changelog.md
new file mode 100644
index 0000000000..1d6106d3a6
--- /dev/null
+++ b/docs/content/changelog.md
@@ -0,0 +1,4 @@
+# What's new
+
+```{include} ../../CHANGELOG.md
+```
diff --git a/docs/content/changelog.rst b/docs/content/changelog.rst
deleted file mode 100644
index 0985a445a1..0000000000
--- a/docs/content/changelog.rst
+++ /dev/null
@@ -1,59 +0,0 @@
-Changes in deepTools4.0
-=======================
-
-Plotting
---------
-
-* Plots in general:
-    - Removed Plotly for all graphics.
-	- Optional ggplot theme (--ggplot).
-	- Using standard Matplotlib color scheme.
-
-* plotHeatmap and plotProfile:
-	- Adjusted the legend position to be outside the plot area, preventing overlap with the subplots.
-	- Split and wrapped longer sample names to avoid overlap with other labels.
-	- Eliminated overlapping x and y-axis ticks for improved readability.
-	- Removed the file extensions from input files when using them as labels in the plots.
-
-* plotEnrichment:
-	- Added spacing between bars in bar plots for improved visual clarity.
-	- Retained only sample names, when provided with the complete file path and name.
-
-* plotPCA:
-    - Re-implemented with a lightweight scipy/numpy SVD backend (mirroring scikit-learn's PCA), instead of the previous plotly-based implementation.
-	- New option to add labels for each point (--addLabels).
-	- Expander for colors and markers, for example ``--colors red:3 blue:3`` is expanded as ``[red, red, red, blue, blue, blue]``.
-	- Scree plot is showing lines for individual and accumulated variation.
-	- Points are by default rainbow colored circles.
-
-Core
-----
-
-* bamCoverage
-    - --no_collapse flag to not merge bins with equal coverage values together.
- 
-* computeMatrix
-    - Sorting ascend / descend no longer has subsorting by position.
-    - --quiet / -q option no longer exists.
-    - bed files in computeMatrix no longer support '#' to define groups.
-    - 'chromosome matching' i.e. chr1 <-> 1, chrMT <-> MT is no longer performed.
-	- metagene mode erroneously 'nan'ed the before and after values (if they fell outside of the feature). This is fixed now.
-	- Rounding bahvior in matrix output only two decimals now, unscaled 5 and unscaled 3 prime are now strictly separated from the rest of the scaled region (for value calculation).
-	
-* normalization
-    - Exactscaling is no longer an option, it's always performed.
-	- SES option in bamCompare mode is no longer available.
-	- blackList filtering is now performed on a position-based level. Meaning reads that overlap partially with the blacklist can still contribute to the signal.
-
-* alignmentSieve
-    - --genomeChunkLength is removed; --label, --smartLabels and --ignoreDuplicates are still available.
-    - output order now exactly matches input order.
-
-* new Rust-backed core
-    - bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary are now backed by a Rust core (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations.
-    - the previous Python implementations remain available as ``bamCoverage_old``, ``bamCompare_old``, ``computeMatrix_old``, ``alignmentSieve_old`` and ``multiBamSummary_old`` during the transition, but will be removed in a future release.
-    - gzipped GTF/BED region files are now supported in multiBamSummary, computeMatrix and alignmentSieve; gzipped blacklist files are supported in all five Rust-backed tools.
-    - large scale values have slightly different precision than before (f32 vs f64 internally).
-
-Testing
--------
diff --git a/pixi.lock b/pixi.lock
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 - pypi: https://files.pythonhosted.org/packages/01/c4/4fa4c8b3097a11f3c5f09a35b72ed6855fb1d332469504962ab7bafcc702/charset_normalizer-3.4.9-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
   name: charset-normalizer
@@ -9074,6 +9099,43 @@ packages:
   - beautifulsoup4 ; extra == 'htmlsoup'
   - lxml-html-clean ; extra == 'html-clean'
   requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/09/dc/f3dfb7488b770f3f67e6545085bf2abea5172e88f57b8ad25ef860ca704c/myst_parser-5.1.0-py3-none-any.whl
+  name: myst-parser
+  version: 5.1.0
+  sha256: 9c91c52b3cdb4d94a6506e4fab4e2f296c7623a0da0dcbe6de1565c3dad67a8a
+  requires_dist:
+  - docutils>=0.20,<0.23
+  - jinja2
+  - markdown-it-py~=4.2
+  - mdit-py-plugins~=0.6,>=0.6.1
+  - pyyaml
+  - sphinx>=8,<10
+  - pre-commit~=4.0 ; extra == 'code-style'
+  - linkify-it-py~=2.0 ; extra == 'linkify'
+  - sphinx>=8 ; extra == 'rtd'
+  - ipython ; extra == 'rtd'
+  - sphinx-book-theme~=1.1 ; extra == 'rtd'
+  - sphinx-design ; extra == 'rtd'
+  - sphinx-copybutton ; extra == 'rtd'
+  - sphinxext-rediraffe~=0.3.0 ; extra == 'rtd'
+  - sphinxext-opengraph~=0.13.0 ; extra == 'rtd'
+  - sphinx-pyscript ; extra == 'rtd'
+  - sphinx-tippy>=0.4.3 ; extra == 'rtd'
+  - sphinx-autodoc2~=0.5.0 ; extra == 'rtd'
+  - sphinx-togglebutton ; extra == 'rtd'
+  - beautifulsoup4 ; extra == 'testing'
+  - coverage[toml] ; extra == 'testing'
+  - defusedxml ; extra == 'testing'
+  - pytest>=9,<10 ; extra == 'testing'
+  - pytest-cov ; extra == 'testing'
+  - pytest-regressions ; extra == 'testing'
+  - pytest-param-files~=0.6.0 ; extra == 'testing'
+  - sphinx-pytest~=0.3.0 ; extra == 'testing'
+  - pygments<2.21 ; extra == 'testing'
+  - pygments ; extra == 'testing-docutils'
+  - pytest>=9,<10 ; extra == 'testing-docutils'
+  - pytest-param-files~=0.6.0 ; extra == 'testing-docutils'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/0a/20/e022dbc6b4753a9bc9fc5fb28a27163430c1731b9913997f6544c1b2518c/lxml-6.1.3-cp312-cp312-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl
   name: lxml
   version: 6.1.3
@@ -12047,6 +12109,21 @@ packages:
   version: 3.5.1
   sha256: e90251c0c7bdd54a100a0dce3c07b7e637278c93af29dbf78ebb89a58c4bac7d
   requires_python: '>=3.7'
+- pypi: https://files.pythonhosted.org/packages/a5/69/6da5581c6a7fede7dc261bf4e67d6adca4196f176b43288b55b3db395b6e/mdit_py_plugins-0.6.1-py3-none-any.whl
+  name: mdit-py-plugins
+  version: 0.6.1
+  sha256: 214c82fb2ac524472ab6a5bcab1de80f73b50443e187f401bfd77efbc7c6481d
+  requires_dist:
+  - markdown-it-py>=2.0.0,<5.0.0
+  - pre-commit ; extra == 'code-style'
+  - myst-parser ; extra == 'rtd'
+  - sphinx-book-theme ; extra == 'rtd'
+  - coverage ; extra == 'testing'
+  - pytest ; extra == 'testing'
+  - pytest-cov ; extra == 'testing'
+  - pytest-regressions ; extra == 'testing'
+  - pytest-timeout ; extra == 'testing'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/a6/ed/c5510c615dce55b6fcc364aa1838142f938beed64f5e4927490dfcaf4405/nh3-0.3.7-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: nh3
   version: 0.3.7
diff --git a/pyproject.toml b/pyproject.toml
index 02bd3ebf90..c3b1438cda 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,6 +66,7 @@ docs = [
     "mock >= 5.1.0",
     "sphinx_rtd_theme >= 2.0.0",
     "sphinx-argparse >= 0.4.0",
+    "myst-parser >= 3.0.0",
 ]
 [project.urls]
 homepage = "https://pypi.python.org/pypi/deepTools/"