GitHub

Cell-GPS is the Python package and reference implementation for Cophenetic Spatial Topology Embedding (COSTE), a spatial topology analysis framework for spatial omics data.

If you use the Python package, the Windows executable, the R companion package, or the manuscript figure/table code, please cite this preprint.
GitHub

C++ fast hierarchical clustering algorithms

This is a simplified C++ interface to the fast implementations of hierarchical clustering by Daniel Müllner. The original library with interfaces to R and Python can be found on danifold.net and is ...
C&EN

Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java

Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator. Mass spectrometry is a powerful technique for analyzing molecules in complex ...
PNAS

Computational inference of eIF4F complex function and structure in human cancers

To understand the importance of eIF4F components, we employed computational methods on large public datasets to investigate the impact of positive selection on eIF4F dysregulation in cancer. By ...
Frontiers

Retinal astrocyte morphology predicts integration of vascular and neuronal architecture

Astrocytes are important regulators of blood flow and play a key role in the response to injury and disease in the central nervous system (CNS). Despite having an understanding that structural changes ...
Frontiers

PyRAT: An Open-Source Python Library for Animal Behavior Analysis

Here we developed an open-source Python-based library called Python rodent Analysis and Tracking (PyRAT). Our library analyzes tracking data to classify distinct behaviors, estimate traveled distance, ...