Make sure torch is installed: https://pytorch.org/get-started/locally/
python3 -m venv gvenv
source gvenv/bin/activate
python3 setup.py install
from genevector.data import GeneVectorDataset
from genevector.model import GeneVectorTrainer
from genevector.embedding import GeneEmbedding, CellEmbedding
import scanpy as sc
dataset = GeneVectorDataset(adata, device="cuda")
cmps = GeneVector(dataset,
output_file="genes.vec",
emb_dimension=100,
initial_lr=0.1,
device="cuda")
cmps.train(200) # run for 200 iterations
gembed = GeneEmbedding("genes.vec", dataset, vector="average")
cembed = CellEmbedding(dataset, gembed)
gembed.compute_similarities("CD8A")
cembed.batch_correct(column="sample")
adata = cembed.get_adata()
gdata = embed.get_adata()
metagenes = embed.get_metagenes(gdata)