scenicplus.yml

### Anaconda environment for analysis
### To install,
###    mamba env create --file=scenicplus.yml

name: scenicplus

channels:
  - conda-forge
  - bioconda

dependencies:
  - conda-forge::python==3.8
  - conda-forge::pandas>=1.3.5
  - conda-forge::numpy
  - conda-forge::tqdm
  - conda-forge::ray-core
  - conda-forge::attr
  - conda-forge::typing
  - conda-forge::matplotlib
  - conda-forge::scikit-learn>=0.22.2
  # - conda-forge::statistics
  - bioconda::pyranges
  - conda-forge::scipy
  - bioconda::pybiomart
  - conda-forge::requests
  - bioconda::arboreto>=0.1.6
  - bioconda::gseapy==0.10.8
  - conda-forge::networkx
  - conda-forge::seaborn
  - bioconda::pyBigWig
  - conda-forge::plotly
  - conda-forge::adjustText
  - bioconda::macs2
  - conda-forge::lxml
  - bioconda::tspex
  - conda-forge::kaleido-core
  - conda-forge::pyvis
  - conda-forge::pygam
  - conda-forge::scanpy~=1.9
  - conda-forge::cython
  - conda-forge::plotnine
  - conda-forge::mudata
  - conda-forge::sphinx_rtd_theme
  - conda-forge::nbsphinx
  - conda-forge::nbsphinx-link
  - conda-forge::numpydoc
  - conda-forge::sphinx-book-theme
  - conda-forge::pip
  ### pycisTopic:
  - conda-forge::python-annoy
  - bioconda::bbknn
  - conda-forge::ipython
  - conda-forge::ipykernel
  - conda-forge::gensim
  - bioconda::harmonypy
  - conda-forge::ipympl
  - conda-forge::leidenalg
  - conda-forge::pbr ## req for lda, which conda-forge doesn't have correctly
  # - conda-forge::lda
  # - conda-forge::loompy==3.0.7 ### conda-forge has not updated recently
  - conda-forge::pyopenssl
  - conda-forge::polars>=0.11.0
  - bioconda::pybedtools
  - bioconda::pyfasta
  - conda-forge::python-levenshtein
  - bioconda::scanorama
  - bioconda::scrublet
  - conda-forge::statsmodels
  - conda-forge::pytables
  - conda-forge::umap-learn
  - conda-forge::xlrd
  - conda-forge::papermill
  - conda-forge::bs4
  - conda-forge::pyarrow
  ### pyscenic
  - conda-forge::cytoolz
  - conda-forge::aiohttp
  - conda-forge::llvmlite
  - conda-forge::numba>=0.51.2
  - conda-forge::attrs
  - conda-forge::frozendict
  - conda-forge::numexpr
  - conda-forge::cloudpickle
  - conda-forge::dask
  - conda-forge::distributed
  - conda-forge::boltons
  - conda-forge::pyyaml
  - conda-forge::interlap
  - conda-forge::fsspec
  ## other
  - conda-forge::ply
  - conda-forge::pandoc
  - conda-forge::globre
  - conda-forge::numpy_groupies
  - pip:
      - git+https://github.com/aertslab/pycisTopic@master#egg=pycisTopic
      - git+https://github.com/aertslab/pycistarget@master#egg=pycistarget
      - git+https://github.com/aertslab/pySCENIC@master#egg=pyscenic
      - git+https://github.com/aertslab/LoomXpy@main#egg=loomxpy
      - ctxcore>=0.2.0
      - tmtoolkit
      - multiprocessing_on_dill
      - lda