A single-cell RNA sequencing environment in python

environment.yml

name: scRNAseq
channels:
  - conda-forge
  - bioconda
  - nvidia
dependencies:
  - python=3.10
  - IPython=8.14
  - ipykernel=6.23
  - ipywidgets=8.0
  - jupyter=1.0.0
  - jupyter-cache=0.6
  - nbformat=5.9
  - nbclient>0.5
  - pandas=2.0
  - numpy>1.23
  - scipy=1
  - matplotlib=3.7
  - seaborn=0.12
  - plotly=5.15
  - pytorch=2.0
  - scanpy=1.9
  - scvi=0.6
  - scvi-tools=1.0
  - scikit-learn
  - tqdm=4.65
  - requests=2.31
  - urllib3
  - six=1.16
  - datalad=0.19
  - arrow=1.2
  - fastparquet=2023.4
  - pandoc=3.1
  - nbconvert=7.6
  - papermill=2.3
  - pytorch=2.0
  - pygraphviz=1.11
  - jaxlib=*=*cuda*
  - jax
  - cuda-nvcc
  - gseapy=1.0
  - scikit-image=0.20
  - scikit-misc=0.1
  - h5py>3
  - click>8.1
  - python-igraph=0.10
  - leidenalg=0.9
  - tabulate=0.9
  - scvelo=0.2
  - hnswlib=0.7
  - pybind11=2.10
  - louvain=0.8
  - black=23.3
  - black-jupyter=23.3
  - celltypist
  - pydeseq2=0.3
  - lightning=2.0.1
  - cython=0.29.36
  - rpy2=3.5
  - pip
  - pip:
    - velocyto
    - pybind11
    - hnswlib