share environment

README.md

@@ -46,6 +46,7 @@ wget https://storage.googleapis.com/linnarsson-lab-human/ATAC_dev/10X/{sample}
 We use the [Chromograph](https://github.com/linnarsson-lab/chromograph) pipeline.
 
 Code for making many of the figures is available as [Jupyter notebooks](notebooks/README.md)
+The package versions used to generate these figures are in [this environment file](environment.yml)
 
 ### Genes and transcripts annotation
 

environment.yml

@@ -0,0 +1,163 @@
+name: fetal_brain_multiomics
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - ca-certificates=2023.5.7=hbcca054_0
+  - cudatoolkit=11.8.0=h37601d7_11
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=13.1.0=he5830b7_0
+  - libgomp=13.1.0=he5830b7_0
+  - libllvm8=8.0.1=hc9558a2_0
+  - libllvm9=9.0.1=default_hc23dcda_7
+  - libnsl=2.0.0=h7f98852_0
+  - libpng=1.6.39=h753d276_0
+  - libsqlite=3.42.0=h2797004_0
+  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libzlib=1.2.13=hd590300_5
+  - llvm-openmp=16.0.6=h4dfa4b3_0
+  - mysql-connector-c=6.1.11=h6eb9d5d_1007
+  - ncurses=6.4=hcb278e6_0
+  - openssl=1.1.1u=hd590300_0
+  - pip=23.2=pyhd8ed1ab_0
+  - python=3.7.12=hb7a2778_100_cpython
+  - readline=8.2=h8228510_1
+  - setuptools=68.0.0=pyhd8ed1ab_0
+  - sqlite=3.42.0=h2c6b66d_0
+  - tk=8.6.12=h27826a3_0
+  - ucsc-bedgraphtobigwig=445=h954228d_0
+  - ucsc-bigwigaverageoverbed=377=ha8a8165_3
+  - ucsc-genepredtobed=447=h954228d_0
+  - ucsc-gtftogenepred=447=h954228d_0
+  - wheel=0.40.0=pyhd8ed1ab_1
+  - xz=5.2.6=h166bdaf_0
+  - zlib=1.2.13=hd590300_5
+  - zstd=1.5.2=hfc55251_7
+  - pip:
+      - aiohttp==3.8.4
+      - aiosignal==1.3.1
+      - argcomplete==3.1.1
+      - argh==0.27.2
+      - asciitree==0.3.3
+      - async-timeout==4.0.2
+      - asynctest==0.13.0
+      - attrs==23.1.0
+      - backcall==0.2.0
+      - biopython==1.81
+      - bx-python==0.9.0
+      - captum==0.6.0
+      - certifi==2023.5.7
+      - charset-normalizer==3.2.0
+      - click==8.1.5
+      - cooler==0.9.2
+      - cycler==0.11.0
+      - cython==0.29.36
+      - cytoolz==0.12.1
+      - debugpy==1.6.7
+      - decorator==5.1.1
+      - deeplift==0.6.13.0
+      - dill==0.3.6
+      - entrypoints==0.4
+      - exceptiongroup==1.1.2
+      - fisher==0.1.10
+      - fonttools==4.38.0
+      - frozenlist==1.3.3
+      - fsspec==2023.1.0
+      - future==0.18.3
+      - gffutils==0.12
+      - h5py==3.8.0
+      - harmony-pytorch==0.1.7
+      - hdbscan==0.8.30
+      - hicmatrix==15
+      - idna==3.4
+      - igraph==0.10.6
+      - importlib-metadata==6.7.0
+      - iniconfig==2.0.0
+      - intervaltree==3.1.0
+      - ipykernel==6.16.2
+      - ipython==7.34.0
+      - jedi==0.18.2
+      - joblib==1.3.1
+      - jupyter-client==7.4.9
+      - jupyter-core==4.12.0
+      - kiwisolver==1.4.4
+      - kneed==0.8.5
+      - leidenalg==0.10.0
+      - lightning-utilities==0.9.0
+      - llvmlite==0.34.0
+      - loompy==3.0.7
+      - macs2==2.2.8
+      - matplotlib==3.5.3
+      - matplotlib-inline==0.1.6
+      - multidict==6.0.4
+      - multiprocess==0.70.14
+      - nest-asyncio==1.5.6
+      - networkx==2.6.3
+      - numba==0.51.0
+      - numexpr==2.8.4
+      - numpy==1.21.6
+      - numpy-groupies==0.9.6
+      - nvidia-cublas-cu11==11.10.3.66
+      - nvidia-cuda-nvrtc-cu11==11.7.99
+      - nvidia-cuda-runtime-cu11==11.7.99
+      - nvidia-cudnn-cu11==8.5.0.96
+      - opentsne==1.0.0
+      - packaging==23.1
+      - pandas==1.3.5
+      - parso==0.8.3
+      - patsy==0.5.3
+      - pexpect==4.8.0
+      - pickleshare==0.7.5
+      - pillow==9.5.0
+      - pluggy==1.2.0
+      - prompt-toolkit==3.0.39
+      - psutil==5.9.5
+      - ptyprocess==0.7.0
+      - pybedtools==0.9.0
+      - pybigwig==0.3.22
+      - pyfaidx==0.7.2.1
+      - pygenometracks==3.8
+      - pygments==2.15.1
+      - pynndescent==0.4.8
+      - pyparsing==3.1.0
+      - pysam==0.21.0
+      - pytest==7.4.0
+      - python-dateutil==2.8.2
+      - python-louvain==0.16
+      - pytorch-lightning==1.9.5
+      - pytz==2023.3
+      - pyyaml==6.0
+      - pyzmq==25.1.0
+      - requests==2.31.0
+      - scikit-learn==1.0.2
+      - scikit-network==0.28.2
+      - scipy==1.7.3
+      - seaborn==0.12.2
+      - simplejson==3.19.1
+      - six==1.16.0
+      - sortedcontainers==2.4.0
+      - statsmodels==0.13.5
+      - tables==3.7.0
+      - texttable==1.6.7
+      - threadpoolctl==3.1.0
+      - tomli==2.0.1
+      - toolz==0.12.0
+      - torch==1.12.1
+      - torchmetrics==0.11.4
+      - tornado==6.2
+      - tqdm==4.65.0
+      - traitlets==5.9.0
+      - twobitreader==3.1.7
+      - typing-extensions==4.7.1
+      - umap-learn==0.4.6
+      - unidip==0.1.1
+      - urllib3==2.0.3
+      - wcwidth==0.2.6
+      - yarl==1.9.2
+      - zipp==3.15.0
+prefix: /home/camiel/anaconda3/envs/fetal_brain_multiomics