scgraph is a collection of graph-based algorithms for the analysis of high-dimensional, high-throughput data, with a particular focus on single-cell genomics. scgraph currently contains methods for running:
You can install scgraph with pip:
pip install --user git+https://github.com/KrishnaswamyLab/scgraph
You can use scgraph as follows:
import scprep
import scgraph
data = scprep.io.load_csv("my_data.csv")
data_graph = scgraph.Graph(data)
data_phate = scgraph.PHATE().fit_transform(data_graph)
data_magic = scgraph.MAGIC().fit_transform(data, graph=data_graph)
signal = scprep.io.load_csv("metadata.csv")
data_meld = scgraph.MELD().fit_transform(RES=signal, G=data_graph)