Our team is developing specialized software designed to work with big biological and medical data. Examples of our successful software developments are the R/C++ and Java packages ORFhunteR, CelNetAnalyzer and RNAexploreR, as well as the CellDataMiner software package.
ORFhunteR
ORFhunteR is designed to automatically detect and annotate open reading frames in large sets of human RNA sequences, including RNA molecules assembled from whole transcriptome sequencing data. A more detailed description of the software is given in the article Vasily V. Grinev, Mikalai M. Yatskou, Victor V. Skakun, Maryna K. Chepeleva, Petr V. Nazarov. ORFhunteR: An accurate approach to the automatic identification and annotation of open reading frames in human mRNA molecules. // Software Impacts. – 2022. – Vol. 12. – Article 100268. The package is available via GitHub, Bioconductor or as Web-application.
CelNetAnalyzer
CelNetAnalyzer is an easy-to-use software package written in the Java programming language. The package is designed for topological analysis of large undirected molecular networks of a cell. CelNetAnalyzer is controlled using a graphical user interface. At the output, the package outputs the values of various topological indices characterizing the state of the network: degree index, neighborhood index, clustering index, distance index, centrality index, heterogeneity index, simple cycles, compositional complexity, Shannon information entropy. Comparative studies have shown that CelNetAnalyzer performs all calculations much faster than competing software products. This is ensured by parallelization of calculations, improvement of existing algorithms, as well as the introduction of new, more efficient analysis algorithms. The package is available for non-commercial use as a freely downloadable archive containing the GUI version of the program, source code, user manual and reference network for testing the program . CelNetAnalyzer requires JavaTM Platform Standard Edition version 6 or higher to function correctly.
RNAexploreR
A package of computer programs written in the R programming language. The RNAexploreR package includes a number of original R-functions that allow analyzing the structure and predicting new RNA isoforms of human genes. The current version of the pipeline is based on the analysis of RNA products of the human RUNX1/RUNX1T1 hybrid oncogene. The package is freely available as Web-application implemented using Shiny technology.
CellDataMiner
The CellDataMiner software package is designed for object segmentation on immunohistochemical luminescent images of cancer cells and analysis of isolated cell populations at the pixel level, followed by the use of classification and clustering methods to isolate groups of cancer cells.
These and our other software developments can be used in both fundamental and applied research, including personalized medicine. We will be happy to discuss options for cooperation in the development of new software for your goals and objectives.