REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and algorithms
Python 3.8.13	Van Rossum et al.64	https://www.python.org/
Numpy 1.21.6	Harris et al.65	https://numpy.org/
Pandas 1.4.2	McKinney et al.66	https://pandas.pydata.org/
Matplotlib 3.5.2	Hunter et al.67	https://matplotlib.org/
Scanpy 1.9.1	Wolf et al.68	https://github.com/scverse/scanpy
Scikit-learn 1.1.1	Pedregosa et al.69	https://scikit-learn.org/stable/index.html
Scipy 1.8.1	Virtanen et al.70	https://scipy.org/
Statsmodels 0.13.2	Seabold et al.71	https://www.statsmodels.org/stable/index.html
Dask/Distributed 2022.7.0	Rocklin et al.72	https://dask.org
Pyitlib 0.2.2	Peter Foster and Michael Milton73	https://github.com/pafoster/pyitlib
Leidenalg 0.8.10	Traag et al.40	https://leidenalg.readthedocs.io/en/stable/
Python_igraph 0.9.11	Csardi et al.74	https://igraph.org/
Networkx 2.8.3	Hagberg et al.75	https://networkx.org/
Ctxcore 0.1.1	Bravo González-Blas et al.76	https://ctxcore.readthedocs.io/en/latest/
Pyscenic 0.11.2	Aibar et al.19	https://scenic.aertslab.org/
R 4.1.2	R Core Team (2022).77	https://www.r-project.org/
enrichR 3.0	Kuleshov et al.78	https://www.rdocumentation.org/packages/enrichR/versions/3.0
Ppcor	Kim, 201516	https://www.rdocumentation.org/packages/ppcor/versions/1.1
PIDC	Chan et al., 201717	https://github.com/Tchanders/NetworkInference.jl
GRNBOOST2	Moerman et al., 201918	https://arboreto.readthedocs.io/en/latest/installation.html
Random Walk	Huang et al., 201835	https://github.com/idekerlab/Network_Evaluation_Tools
SCING	This paper/GitHub	https://github.com/XiaYangLabOrg/SCING
Deposited data
Human Alzheimer’s Disease snRNAseq	Morabito et al., 202127	https://www.synapse.org/#!Synapse:syn22079621/
Dendritic cell and k562 cell line perturb-seq datasets	Dixit et al., 201632	GEO: GSE90063
THP-1 cells	Papalexi et al., 202131	GEO: GSE153056
Mouse Cell Atlas	Han et al., 201826	https://bis.zju.edu.cn/MCA/
DisGeNET	Piñero et al., 201979	http://www.disgenet.org/
Mouse AD Visium	Chen et al., 202028	GEO: GSE152506