GitHub

StereoSiTE - Spatial Transcriptome Analysis in Python

Cellular Neighborhood (CN) clustering based on cellular composition of each bin Spatial Cell Interaction Intensity (SCII) analysis Tissue domain clustering based on intercellular interactions within ...
PNAS

Unraveling the mesoscale organization induced by network-driven processes

Understanding how intricate dynamic patterns emerge from complex structural interactions is a formidable challenge. Often, the problem is simplified by focusing on either the structure or dynamics of ...
Nature

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional ...
Nature

Identification of molecular mechanisms causing skin lesions of cutaneous leishmaniasis using weighted gene coexpression network analysis (WGCNA)

Leishmaniasis is caused by protozoan Leishmania parasites from over 20 Leishmania species that are transmitted via the bite of over 90 sandflies species of the infected female ones. Cutaneous ...
Frontiers

Metastable Resting State Brain Dynamics

Data from N = 30 healthy subjects (14 males) with age between 22 and 35 were used in this study. Data were provided by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David ...