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env.yml
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env.yml
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name: pyre
channels:
- conda-forge
- bioconda
- plotly
- nodefaults
dependencies:
# Python
- python>=3.6.1
- pandas
- rpy2
- openpyxl
- matplotlib
- seaborn
- scikit-learn
- scipy
- umap-learn
- chart-studio
- pip
# Jupyter
- jupyter
## nbconvert >=6.0 causes problems
- nbconvert=5.6.1
- nb_conda_kernels
## After install jupyter_contrib_nbextensions, run: jupyter nbextensions_configurator enable --user
- jupyter_contrib_nbextensions
# Command line
- wget
# R
- r-base>=4.0.0
- r-essentials
- r-devtools
- r-reticulate
- r-patchwork
- r-r.methodss3
- r-brew
- r-zip
- r-credentials
- r-sessioninfo
- r-promises
- r-roxygen2
- r-gert
- r-r.oo
- r-rversions
- r-rcmdcheck
- r-usethis
- r-here
- r-openxlsx
- r-r.utils
- r-data.table
- r-ggplot2
- r-tidyverse
- r-uwot
- r-biocmanager
- radian