diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8ff0d0d..8e9a84b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
   - id: trailing-whitespace
   - id: no-commit-to-branch
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.10
+  rev: v0.14.11
   hooks:
   - id: ruff-check
     args: [--fix, --exit-non-zero-on-fix]
@@ -34,28 +34,28 @@ repos:
     language_version: '3.13'
     additional_dependencies:
     - alabaster==1.0.0
-    - anndata==0.12.6
-    - array-api-compat==1.12.0
+    - anndata==0.12.7
+    - array-api-compat==1.13.0
     - babel==2.17.0
-    - certifi==2025.11.12
+    - certifi==2026.1.4
     - cffi==2.0.0
     - charset-normalizer==3.4.4
     - click==8.3.1
     - cloudpickle==3.1.2
     - colorama==0.4.6 ; sys_platform == 'win32'
-    - coverage==7.13.0
-    - dask==2025.11.0
-    - docutils==0.22.3
+    - coverage==7.13.1
+    - dask==2025.12.0
+    - docutils==0.22.4
     - donfig==0.8.1.post1
     - execnet==2.1.2
-    - fsspec==2025.12.0
-    - google-crc32c==1.7.1
+    - fsspec==2026.1.0
+    - google-crc32c==1.8.0
     - h5py==3.15.1
     - idna==3.11
     - imagesize==1.4.1
     - iniconfig==2.3.0
     - jinja2==3.1.6
-    - joblib==1.5.2
+    - joblib==1.5.3
     - legacy-api-wrap==1.5
     - llvmlite==0.46.0
     - locket==1.0.0
@@ -76,20 +76,20 @@ repos:
     - pygments==2.19.2
     - pytest==9.0.2
     - pytest-codspeed==4.2.0
-    - pytest-doctestplus==1.6.0
+    - pytest-doctestplus==1.7.0
     - pytest-xdist==3.8.0
     - python-dateutil==2.9.0.post0
     - pytz==2025.2
     - pyyaml==6.0.3
     - requests==2.32.5
     - rich==14.2.0
-    - roman-numerals==3.1.0
+    - roman-numerals==4.1.0
     - scikit-learn==1.8.0
-    - scipy==1.16.3
-    - scipy-stubs==1.16.3.3
+    - scipy==1.17.0
+    - scipy-stubs==1.17.0.0
     - six==1.17.0
     - snowballstemmer==3.0.1
-    - sphinx==9.0.4
+    - sphinx==9.1.0
     - sphinxcontrib-applehelp==2.0.0
     - sphinxcontrib-devhelp==2.0.0
     - sphinxcontrib-htmlhelp==2.1.0
@@ -99,8 +99,8 @@ repos:
     - threadpoolctl==3.6.0
     - toolz==1.1.0
     - types-docutils==0.22.3.20251115
-    - tzdata==2025.2
-    - urllib3==2.6.1
+    - tzdata==2025.3
+    - urllib3==2.6.3
     - zarr==3.1.5
 ci:
   autoupdate_commit_msg: 'ci: pre-commit autoupdate'