Welcome to DECNEO documentation!

DECNEO (DEndrogram of Co-expression with Evolutionary Conservation and Network Enrichment Ordering) is a new software tool that identifies general and tissue-specific receptor comberons in endothelial cells and provides visualization and statistical analysis.

Note

DECNEO is introduced in:

Comberons from single cell transcriptomics in endothelial cells. Sergii Domanskyi, Alex Hakansson, Michelle Meng, Joshua S Graff Zivin, Carlo Piermarocchi, Giovanni Paternostro, Napoleone Ferrara, in review (2021). BioRxiv preprint: https://doi.org/10.1101/2021.01.04.425317

The pipeline shown in Overview is implemented in our new software DECNEO. We have developed a main and an alternative implementation of DECNEO that are open-source and maintained at https://github.com/sdomanskyi/decneo. Releases are published on the Zenodo archive at https://doi.org/10.5281/zenodo.4417915.

The main implementation can be installed from PyPI using the command pip install decneo, see Getting Started. DECNEO modules are relying on Python numpy, scipy, pandas, scikit-learn, matplotlib and other packages (see Dependency graph for dependencies). The main implementation can leverage on a multicore large-memory High-Performance Computing Systems for fast processing of large datasets. The software was optimized for use with the HPCC supercomputer at Michigan State University but also tested on different operating systems and hardware.

See also

The source code of the alternative implementation is deposited at https://github.com/sdomanskyi/decneo/validation.

Contents

• Overview
  • Description of the package functionality
  • Versions change log
• Getting Started
  • Installation
  • Loading the package
• Core class API
• Dependency graph
• Input data format
• Examples
• Output data
  • Directories
  • Files

Indices and tables

• Index

• Module Index

• Search Page