diff --git a/R/basilisk.R b/R/basilisk.R
index 9c81a79..765784d 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -1,168 +1,121 @@
 ## Windows ----
 
 .scvelo.dependencies.Windows <- list(
-  channels = c("conda-forge", "bioconda"),
+  channels = c("conda-forge"),
   packages = c(
-    'anndata==0.9.2',
-    'array-api-compat==1.8',
     'brotli==1.1.0',
     'brotli-bin==1.1.0',
-    'brotli-python==1.1.0',
     'bzip2==1.0.8',
     'ca-certificates==2024.7.4',
-    'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.7.4',
-    'cffi==1.17.0',
-    'charset-normalizer==3.3.2',
-    'click==8.1.7',
-    'colorama==0.4.6',
-    'contourpy==1.1.1',
-    'cycler==0.12.1',
-    'exceptiongroup==1.2.2',
-    'fonttools==4.53.1',
     'freetype==2.12.1',
-    'get-annotations==0.1.2',
-    'gettext==0.22.5',
-    'gettext-tools==0.22.5',
-    'glib==2.80.2',
-    'glib-tools==2.80.2',
-    'gst-plugins-base==1.21.3',
-    'gstreamer==1.21.3',
-    'h2==4.1.0',
-    'h5py==3.9.0',
-    'hdf5==1.14.0',
-    'hpack==4.0.0',
-    'hyperframe==6.0.1',
-    'icu==70.1',
-    'idna==3.7',
-    'importlib-metadata==8.4.0',
-    'importlib-resources==6.4.4',
-    'importlib_resources==6.4.4',
+    'hdf5==1.14.3',
     'intel-openmp==2024.2.1',
-    'joblib==1.4.2',
-    'jpeg==9e',
-    'kiwisolver==1.4.5',
-    'krb5==1.20.1',
-    'lcms2==2.12',
-    'legacy-api-wrap==1.4',
+    'krb5==1.21.3',
+    'lcms2==2.16',
     'lerc==4.0.0',
     'libaec==1.1.3',
-    'libasprintf==0.22.5',
-    'libasprintf-devel==0.22.5',
     'libblas==3.9.0',
     'libbrotlicommon==1.1.0',
     'libbrotlidec==1.1.0',
     'libbrotlienc==1.1.0',
     'libcblas==3.9.0',
-    'libclang==15.0.7',
-    'libclang13==15.0.7',
-    'libcurl==8.1.2',
+    'libcurl==8.9.1',
     'libdeflate==1.21',
     'libexpat==2.6.2',
     'libffi==3.4.2',
-    'libgettextpo==0.22.5',
-    'libgettextpo-devel==0.22.5',
-    'libglib==2.80.2',
     'libhwloc==2.11.1',
     'libiconv==1.17',
-    'libintl==0.22.5',
-    'libintl-devel==0.22.5',
-    'libjpeg-turbo==2.1.4',
+    'libjpeg-turbo==3.0.0',
     'liblapack==3.9.0',
-    'libogg==1.3.5',
     'libpng==1.6.43',
     'libsqlite==3.46.0',
-    'libssh2==1.10.0',
-    'libtiff==4.2.0',
-    'libvorbis==1.3.7',
+    'libssh2==1.11.0',
+    'libtiff==4.6.0',
     'libwebp-base==1.4.0',
     'libxcb==1.16',
     'libxml2==2.12.7',
-    'libzlib==1.2.13',
-    'llvmlite==0.41.1',
-    'loompy==3.0.6',
+    'libzlib==1.3.1',
     'm2w64-gcc-libgfortran==5.3.0',
     'm2w64-gcc-libs==5.3.0',
     'm2w64-gcc-libs-core==5.3.0',
     'm2w64-gmp==6.1.0',
     'm2w64-libwinpthread-git==5.0.0.4634.697f757',
-    'matplotlib==3.7.2',
-    'matplotlib-base==3.7.2',
+    'matplotlib-base==3.9.2',
     'mkl==2024.1.0',
     'msys2-conda-epoch==20160418',
+    'numpy_groupies==0.11.2',
+    'openjpeg==2.5.2',
+    'openssl==3.3.1',
+    'pthread-stubs==0.4',
+    'pthreads-win32==2.9.1',
+    'python==3.12.5',
+    'python-tzdata==2024.1',
+    'python_abi==3.12',
+    'qhull==2020.2',
+    'seaborn-base==0.13.2',
+    'tbb==2021.12.0',
+    'tk==8.6.13',
+    'typing_extensions==4.12.2',
+    'ucrt==10.0.22621.0',
+    'vc==14.3',
+    'vc14_runtime==14.40.33810',
+    'vs2015_runtime==14.40.33810',
+    'xorg-libxau==1.0.11',
+    'xorg-libxdmcp==1.1.3',
+    'xz==5.2.6',
+    'zstd==1.5.6'
+  ),
+  pip = c(
+    'anndata==0.10.9',
+    'array-api-compat==1.8',
+    'cached-property==1.5.2',
+    'certifi==2024.7.4',
+    'click==8.1.7',
+    'colorama==0.4.6',
+    'contourpy==1.3.0',
+    'cycler==0.12.1',
+    'exceptiongroup==1.2.2',
+    'fonttools==4.53.1',
+    'get-annotations==0.1.2',
+    'h5py==3.11.0',
+    'joblib==1.4.2',
+    'kiwisolver==1.4.5',
+    'legacy-api-wrap==1.4',
+    'llvmlite==0.43.0',
+    'loompy==3.0.6',
+    'matplotlib==3.9.2',
     'munkres==1.1.4',
     'natsort==8.4.0',
-    'networkx==3.1',
-    'numba==0.58.1',
-    'numpy==1.24.4',
-    'numpy_groupies==0.9.22',
-    'olefile==0.47',
-    'openjpeg==2.4.0',
-    'openssl==1.1.1w',
+    'networkx==3.3',
+    'numba==0.60.0',
+    'numpy==1.26.4',
+    'numpy-groupies==0.11.2',
     'packaging==24.1',
-    'pandas==2.0.3',
+    'pandas==2.2.2',
     'patsy==0.5.6',
-    'pcre2==10.43',
-    'pillow==8.2.0',
+    'pillow==10.4.0',
     'pip==24.2',
-    'platformdirs==4.2.2',
-    'ply==3.11',
-    'pooch==1.8.2',
-    'pthread-stubs==0.4',
-    'pthreads-win32==2.9.1',
-    'pycparser==2.22',
     'pynndescent==0.5.13',
-    'pyparsing==3.0.9',
-    'pyqt==5.15.7',
-    'pyqt5-sip==12.11.0',
-    'pysocks==1.7.1',
-    'python==3.8.0',
+    'pyparsing==3.1.4',
     'python-dateutil==2.9.0',
-    'python-tzdata==2024.1',
-    'python_abi==3.8',
     'pytz==2024.1',
-    'qhull==2020.2',
-    'qt-main==5.15.6',
-    'requests==2.32.3',
     'scanpy==1.10.2',
-    'scikit-learn==1.3.2',
-    'scipy==1.10.1',
+    'scikit-learn==1.5.1',
+    'scipy==1.14.1',
     'scvelo==0.2.5',
     'seaborn==0.13.2',
-    'seaborn-base==0.13.2',
     'session-info==1.0.0',
     'setuptools==72.2.0',
-    'sip==6.7.12',
     'six==1.16.0',
-    'sqlite==3.46.0',
-    'statsmodels==0.14.1',
+    'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'tbb==2021.12.0',
     'threadpoolctl==3.5.0',
-    'tk==8.6.13',
-    'toml==0.10.2',
-    'tomli==2.0.1',
-    'tornado==6.4.1',
     'tqdm==4.66.5',
-    'typing_extensions==4.12.2',
-    'tzdata==2024a',
-    'ucrt==10.0.22621.0',
+    'typing-extensions==4.12.2',
+    'tzdata==2024.1',
     'umap-learn==0.5.6',
-    'unicodedata2==15.1.0',
-    'urllib3==2.2.2',
-    'vc==14.3',
-    'vc14_runtime==14.40.33810',
-    'vs2015_runtime==14.40.33810',
-    'wheel==0.44.0',
-    'win_inet_pton==1.1.0',
-    'xorg-libxau==1.0.11',
-    'xorg-libxdmcp==1.1.3',
-    'xz==5.2.6',
-    'zipp==3.20.0',
-    'zlib==1.2.13',
-    'zstandard==0.23.0',
-    'zstd==1.5.6'
+    'wheel==0.44.0'
   )
 )
 
@@ -170,6 +123,7 @@
 
 .scvelo.dependencies.MacOSXArm <- list(
   channels = c("conda-forge", "bioconda"),
+  pip = character(0),
   packages = c(
     'absl-py==2.1.0',
     'anndata==0.10.7',
@@ -446,6 +400,7 @@
 
 .scvelo.dependencies.MacOSX <- list(
   channels = c("conda-forge", "bioconda"),
+  pip = character(0),
   packages = c(
     'absl-py==2.1.0',
     'anndata==0.10.7',
@@ -722,6 +677,7 @@
 
 .scvelo.dependencies.Linux <- list(
   channels = c("anaconda", "conda-forge", "bioconda"),
+  pip = character(0),
   packages = c(
     '_libgcc_mutex==0.1',
     '_openmp_mutex==4.5',
@@ -889,4 +845,4 @@ if (basilisk.utils::isWindows()) {
 #' @importFrom basilisk BasiliskEnvironment
 #' @importFrom zellkonverter AnnDataDependencies
 velo.env <- BasiliskEnvironment("env", "velociraptor",
-  packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels)
+  packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels, pip = .scvelo_dependencies$pip)
diff --git a/inst/envs/Windows.yaml b/inst/envs/Windows.yaml
index 0f5321f..98d6283 100644
--- a/inst/envs/Windows.yaml
+++ b/inst/envs/Windows.yaml
@@ -3,168 +3,115 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - brotli=1.1.0=hcfcfb64_1
   - brotli-bin=1.1.0=hcfcfb64_1
-  - brotli-python=1.1.0=py38hd3f51b4_1
   - bzip2=1.0.8=h2466b09_7
   - ca-certificates=2024.7.4=h56e8100_0
   - cached_property=1.5.2=pyha770c72_1
   - freetype=2.12.1=hdaf720e_2
-  - gettext=0.22.5=h5728263_3
-  - gettext-tools=0.22.5=h5a7288d_3
-  - glib=2.80.2=h0df6a38_0
-  - glib-tools=2.80.2=h2f9d560_0
-  - gst-plugins-base=1.21.3=h001b923_1
-  - gstreamer=1.21.3=h6b5321d_1
-  - hdf5=1.14.0=nompi_h97a5375_103
-  - icu=70.1=h0e60522_0
-  - importlib_resources=6.4.4=pyhd8ed1ab_0
+  - hdf5=1.14.3=nompi_h2b43c12_105
   - intel-openmp=2024.2.1=h57928b3_1083
-  - jpeg=9e=h8ffe710_2
-  - krb5=1.20.1=h6609f42_0
-  - lcms2=2.12=h2a16943_0
+  - krb5=1.21.3=hdf4eb48_0
+  - lcms2=2.16=h67d730c_0
   - lerc=4.0.0=h63175ca_0
   - libaec=1.1.3=h63175ca_0
-  - libasprintf=0.22.5=h5728263_3
-  - libasprintf-devel=0.22.5=h5728263_3
   - libblas=3.9.0=23_win64_mkl
   - libbrotlicommon=1.1.0=hcfcfb64_1
   - libbrotlidec=1.1.0=hcfcfb64_1
   - libbrotlienc=1.1.0=hcfcfb64_1
   - libcblas=3.9.0=23_win64_mkl
-  - libclang=15.0.7=default_h3a3e6c3_5
-  - libclang13=15.0.7=default_hf64faad_5
-  - libcurl=8.1.2=h68f0423_0
+  - libcurl=8.9.1=h18fefc2_0
   - libdeflate=1.21=h2466b09_0
   - libexpat=2.6.2=h63175ca_0
   - libffi=3.4.2=h8ffe710_5
-  - libgettextpo=0.22.5=h5728263_3
-  - libgettextpo-devel=0.22.5=h5728263_3
-  - libglib=2.80.2=h0df6a38_0
   - libhwloc=2.11.1=default_h8125262_1000
   - libiconv=1.17=hcfcfb64_2
-  - libintl=0.22.5=h5728263_3
-  - libintl-devel=0.22.5=h5728263_3
-  - libjpeg-turbo=2.1.4=hcfcfb64_0
+  - libjpeg-turbo=3.0.0=hcfcfb64_1
   - liblapack=3.9.0=23_win64_mkl
-  - libogg=1.3.5=h2466b09_0
   - libpng=1.6.43=h19919ed_0
   - libsqlite=3.46.0=h2466b09_0
-  - libssh2=1.10.0=h680486a_3
-  - libtiff=4.2.0=h0c97f57_3
-  - libvorbis=1.3.7=h0e60522_0
+  - libssh2=1.11.0=h7dfc565_0
+  - libtiff=4.6.0=hb151862_4
   - libwebp-base=1.4.0=hcfcfb64_0
-  - libxcb=1.16=hcd874cb_0
-  - libxml2=2.12.7=h283a6d9_1
-  - libzlib=1.2.13=h2466b09_6
+  - libxcb=1.16=h013a479_1
+  - libxml2=2.12.7=h0f24e4e_4
+  - libzlib=1.3.1=h2466b09_1
   - m2w64-gcc-libgfortran=5.3.0=6
   - m2w64-gcc-libs=5.3.0=7
   - m2w64-gcc-libs-core=5.3.0=7
   - m2w64-gmp=6.1.0=2
   - m2w64-libwinpthread-git=5.0.0.4634.697f757=2
-  - matplotlib-base=3.7.2=py38h2d9580e_0
+  - matplotlib-base=3.9.2=py312h90004f6_0
   - mkl=2024.1.0=h66d3029_694
   - msys2-conda-epoch=20160418=1
-  - numpy_groupies=0.9.22=pyhd8ed1ab_0
-  - openjpeg=2.4.0=hb211442_1
-  - openssl=1.1.1w=hcfcfb64_0
-  - pcre2=10.43=h17e33f8_0
+  - numpy_groupies=0.11.2=pyhd8ed1ab_0
+  - openjpeg=2.5.2=h3d672ee_0
+  - openssl=3.3.1=h2466b09_3
   - pthread-stubs=0.4=hcd874cb_1001
   - pthreads-win32=2.9.1=hfa6e2cd_3
-  - pyqt=5.15.7=py38hd6c051e_3
-  - python=3.8.0=hc9e8b01_5
+  - python=3.12.5=h889d299_0_cpython
   - python-tzdata=2024.1=pyhd8ed1ab_0
-  - python_abi=3.8=2_cp38
+  - python_abi=3.12=5_cp312
   - qhull=2020.2=hc790b64_5
-  - qt-main=5.15.6=h068e40c_6
   - seaborn-base=0.13.2=pyhd8ed1ab_2
-  - sqlite=3.46.0=h2466b09_0
-  - tbb=2021.12.0=hc790b64_3
+  - tbb=2021.12.0=hc790b64_4
   - tk=8.6.13=h5226925_1
   - typing_extensions=4.12.2=pyha770c72_0
   - ucrt=10.0.22621.0=h57928b3_0
   - vc=14.3=h8a93ad2_20
-  - vc14_runtime=14.40.33810=ha82c5b3_20
+  - vc14_runtime=14.40.33810=hcc2c482_20
   - vs2015_runtime=14.40.33810=h3bf8584_20
-  - win_inet_pton=1.1.0=pyhd8ed1ab_6
   - xorg-libxau=1.0.11=hcd874cb_0
   - xorg-libxdmcp=1.1.3=hcd874cb_0
   - xz=5.2.6=h8d14728_0
-  - zlib=1.2.13=h2466b09_6
   - zstd=1.5.6=h0ea2cb4_0
   - pip:
-    - anndata==0.9.2
+    - anndata==0.10.9
     - array-api-compat==1.8
-    - brotli==1.1.0
     - cached-property==1.5.2
     - certifi==2024.7.4
-    - cffi==1.17.0
-    - charset-normalizer==3.3.2
     - click==8.1.7
     - colorama==0.4.6
-    - contourpy==1.1.1
+    - contourpy==1.3.0
     - cycler==0.12.1
     - exceptiongroup==1.2.2
     - fonttools==4.53.1
     - get-annotations==0.1.2
-    - h2==4.1.0
-    - h5py==3.9.0
-    - hpack==4.0.0
-    - hyperframe==6.0.1
-    - idna==3.7
-    - importlib-metadata==8.4.0
-    - importlib-resources==6.4.4
+    - h5py==3.11.0
     - joblib==1.4.2
     - kiwisolver==1.4.5
     - legacy-api-wrap==1.4
-    - llvmlite==0.41.1
+    - llvmlite==0.43.0
     - loompy==3.0.6
-    - matplotlib==3.7.2
+    - matplotlib==3.9.2
     - munkres==1.1.4
     - natsort==8.4.0
-    - networkx==3.1
-    - numba==0.58.1
-    - numpy==1.24.4
-    - numpy-groupies==0.9.22
-    - olefile==0.47
+    - networkx==3.3
+    - numba==0.60.0
+    - numpy==1.26.4
+    - numpy-groupies==0.11.2
     - packaging==24.1
-    - pandas==2.0.3
+    - pandas==2.2.2
     - patsy==0.5.6
-    - pillow==8.2.0
+    - pillow==10.4.0
     - pip==24.2
-    - platformdirs==4.2.2
-    - ply==3.11
-    - pooch==1.8.2
-    - pycparser==2.22
     - pynndescent==0.5.13
-    - pyparsing==3.0.9
-    - pyqt5==5.15.7
-    - pyqt5-sip==12.11.0
-    - pysocks==1.7.1
+    - pyparsing==3.1.4
     - python-dateutil==2.9.0
     - pytz==2024.1
-    - requests==2.32.3
     - scanpy==1.10.2
-    - scikit-learn==1.3.2
-    - scipy==1.10.1
+    - scikit-learn==1.5.1
+    - scipy==1.14.1
     - scvelo==0.2.5
     - seaborn==0.13.2
     - session-info==1.0.0
     - setuptools==72.2.0
-    - sip==6.7.12
     - six==1.16.0
-    - statsmodels==0.14.1
+    - statsmodels==0.14.2
     - stdlib-list==0.10.0
     - threadpoolctl==3.5.0
-    - toml==0.10.2
-    - tomli==2.0.1
-    - tornado==6.4.1
     - tqdm==4.66.5
     - typing-extensions==4.12.2
     - tzdata==2024.1
     - umap-learn==0.5.6
-    - unicodedata2==15.1.0
-    - urllib3==2.2.2
     - wheel==0.44.0
-    - win-inet-pton==1.1.0
-    - zipp==3.20.0
-    - zstandard==0.23.0
\ No newline at end of file
diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R
index d147eb2..7eb0776 100644
--- a/inst/envs/format_yaml_to_r.R
+++ b/inst/envs/format_yaml_to_r.R
@@ -1,11 +1,32 @@
 library(yaml)
-yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml")
-r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies)
+yaml_data <- yaml::read_yaml("Windows.yaml")
+
+which_pip_dependencies <- which(sapply(yaml_data$dependencies, function(x) any(names(x) %in% "pip")))
+
+conda_dependencies <- yaml_data$dependencies[-c(which_pip_dependencies)]
+
+conda_dependencies <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , conda_dependencies)
+
+
+message("Conda dependencies:")
 cat(paste0(
   "c(",
   "\n",
-  paste0("  ", "'", r_data, "'", collapse = ",\n"),
+  paste0("  ", "'", conda_dependencies, "'", collapse = ",\n"),
   "\n",
   ")",
   "\n"
 ))
+
+message("pip dependencies:")
+if (length(which_pip_dependencies)) {
+  pip_dependencies <- yaml_data$dependencies[[which_pip_dependencies]]$pip
+  cat(paste0(
+    "c(",
+    "\n",
+    paste0("  ", "'", pip_dependencies, "'", collapse = ",\n"),
+    "\n",
+    ")",
+    "\n"
+  ))
+}