Software

glioblastomaEHRsData

An R package that contains and describes three datasets of electronic health records of patients diagnosed with glioblastoma.

SaturnCoefficient / saturnscore

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

healthyControlsPresenceChecker

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

DBCVindex

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

geoCancerDiagnosticDatasetsRetriever

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

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), 2021, in press.

geneExpressionFromGEO

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

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

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.