Software

DensityBasedClusteringValidation - Julia

A Julia package that implements the DBCV clustering metric (mainly developed by Keivan Motavalli).

HDBSCAN - Julia

A Julia package that implements the HDBSCAN clustering method (mainly developed by Felice Liu).

discoCVI - R

An R package that implements the DISCO metric for internal assessment of clustering results (mainly developed by Amin Entezari).

glioblastomaEHRsData - R

An R package that contains and describes three datasets of electronic health records of patients diagnosed with glioblastoma (mainly developed by Samuele Marelli).

SaturnCoefficient - R / saturnscore - Python

An R package and a Python package for the assessment of UMAP dimensionality reduction.

Davide Chicco, Simone Melzi, Francedsca Gasparini, and Giuseppe Jurman, "The advantages of our proposed Saturn coefficient over continuity and trustworthiness for UMAP dimensionality reduction evaluation". PeerJ Computer Science 12:e3424 (2026) 

healthyControlsPresenceChecker - R

An R package that verifies the presence of data of healthy controls in a gene expression dataset, available on Bioconductor.

DBCVindex - R

An R package that calculates the Density-Based Clustering Validation (DBCV) Index, available on CRAN.

geoCancerDiagnosticDatasetsRetriever - Perl

A Perl package to retrieve diagnostic gene expression datasets of a specific cancer type and derived from specific microarray platforms from Gene Expression Omnibus (GEO), available on CPAN.

geoCancerPrognosticDatasetsRetriever - Perl

A Perl package to retrieve prognostic gene expression datasets of a specific cancer type and derived from specific microarray platforms from Gene Expression Omnibus (GEO), available on CPAN.

Abbas Alameer, Davide Chicco, "geoCancerPrognosticDatasetsRetriever, a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO)". Bioinformatics (Oxford journal), volume 38, issue 6, pages 1761–1763 (March 2022).

geneExpressionFromGEO - R

An R package to easily download gene expression datasets from Gene Expression Omnibus (GEO), available on CRAN.

To read more about geneExpressionFromGEO:

Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis. Methods in Molecular Biology, vol 2401, chapter 12, pages 187-194, Springer Protocols, 2021.

BEHST - R and web application

BEHST (Biological Enrichment of Hidden Sequence Targets), a web application for enhanced genetic enrichment set analysis.

To read more about BEHST:

Davide Chicco, Haixin Sarah Bi, Jüri Reimand, Michael M. Hoffman, "BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions", bioRxiv 168427, 2020 .

Bio-Search Computing - web application

Bio-SeCo, a bioinformatics Search Computing platform able to answer to complex multi-domain biological questions and provide ranked results.

To read more about Bio-SeCo:

Davide Chicco, Marco Masseroli, “Software suite for gene and protein annotation prediction and similarity search”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Special Issue on Databases and Software, vol. 12, issue 4, pp. 837–843, IEEE, 2015.