SCMBench/environments at main · ml4bio/SCMBench

Name	Name	Last commit message	Last commit date
parent directory ..
README.md	README.md
env1_installation.sh	env1_installation.sh
env1_requirements.txt	env1_requirements.txt
env2_installation.sh	env2_installation.sh
env2_requirements.txt	env2_requirements.txt
env3_installation.sh	env3_installation.sh
env3_requirements.txt	env3_requirements.txt
env4_R_install.r	env4_R_install.r
env4_installation.sh	env4_installation.sh

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1. Clone our repository

git clone https://github.com/Susanxuan/SCMBench.git

We have summarized Python/R version and packages needed for each method, users can bash [env]_installation.sh files to install requirements for each method accordingly.

Virtual Envs	Python/R Version	Methods
env1_installation.sh	python=3.8	cobolt;GLUE;Harmony;MMD-MA;MOFA;Pamona;PCA; scJoint;scMDC;scMoMaT;UCE;UnionCom
env2_installation.sh	python=3.11	Geneformer;scFoundation;scVI;TotalVI
env3_installation.sh	python=3.10	scGPT
env4_installation.sh	R=4.3.3	bindSC;Deepmaps;iNMF;liger;Seurat4;Seurat5