diff --git a/README.md b/README.md
index 3dd7504..fa66332 100644
--- a/README.md
+++ b/README.md
@@ -179,4 +179,3 @@ Please use this BibTeX to cite this repository in your publications:
   url          = {https://doi.org/10.5281/zenodo.13135902}
 }
 ```
-
diff --git a/pyproject.toml b/pyproject.toml
index 9ce6aca..2786d88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,17 +24,17 @@ dependencies = [
     'pandas==2.2.2',
     'anndata==0.11',
     'numpy==1.26.4',
-    'scikit-learn>=1.2.2',
+    'scikit-learn>=1.5.0',
     'scipy==1.13.1',
     'gitpython==3.1.43',
     'torch==2.5.1',
     'torchvision==0.20.1',
     'accelerate==0.29.3',
-    'transformers==4.45.1',
+    'transformers==4.48.0',
     'loompy==3.0.7',
     'scib==1.1.5',
     'scikit-misc==0.3.1',
-    'azure-identity==1.16.0',
+    'azure-identity==1.16.1',
     'azure-storage-blob==12.19.1',
     'azure-core==1.30.1',
     'einops==0.8.0',
diff --git a/requirements.txt b/requirements.txt
index 51e7a7d..30c24ec 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,20 +1,20 @@
-requests==2.31.0
+requests==2.32.2
 pandas==2.2.2
 anndata==0.10.7
 numpy==1.26.4
-scikit-learn==1.2.2
+scikit-learn==1.5.0
 scipy==1.13.1
 gitpython==3.1.43
 torch>=2.0.0,<=2.3.0
 torchvision>=0.15.0,<=0.18.0
 accelerate==0.29.3
-transformers==4.45.1
+transformers==4.48.0
 loompy==3.0.7
 scib==1.1.5
 scikit-misc==0.3.1
 datasets==2.14.7
 azure-storage-blob==12.19.1
-azure-identity==1.16.0
+azure-identity==1.16.1
 azure-core==1.30.1
 einops==0.8.0
 omegaconf==2.3.0