OmicSDK-Transcriptomics: A Web Platform for Transcriptomics Data Analysis.

Omics sciences, especially transcriptomics, have grown exponentially since the first human genome was sequenced in 2003. Different tools have been developed in the past years for the analysis of this kind of data, but many of them require specific programming knowledge to be used. In this paper, we present omicSDK-transcriptomics, the transcriptomics module of OmicSDK, a comprehensive tool for omics data analysis that combines pre-processing, annotation and visualization tools to be used with omics data. OmicSDK comprises a command-line tool and a user-friendly web solution, so researchers having different backgrounds can take advantage of all its functionalities.

COVID-BIOCHIP: A Web Tool to Analyse COVID-19 Antigen Microarrays.

During the COVID-19 pandemic, there was a growing need to characterise the disease. A very important aspect is the ability to measure the immunisation extent, which can be achieved using antigen microarrays that quantitively measure the presence of COVID-related antibodies. A significant limitation for these tests was the complexity of manually analysing the results, and the limited availability of software for its analysis. In this paper, we describe the development of COVID-BIOCHIP, an ad-hoc web-based solution for the automatic analysis and visualisation of COVID-19 antigen microarray data results.

Development of an Expert Knowledge-Based Genomic Variant Prioritisation Platform.

Considering the growing interest towards next generation sequencing (NGS) and data analysis, and the substantial challenges associated to fully exploiting these technologies and data without the proper experience, an expert knowledge-based user-friendly analytical tool was developed to allow non-bioinformatics experts to process NGS genomic data, automatically prioritise genomic variants and make their own annotations. This tool was developed using a user-centred methodology, where an iterative process was followed until a useful product was developed. This tool allows the users to set-up the pre-processing pipeline, filter the obtained data, annotate it using external and local databases (DBs) and help on deciding which variants are more relevant for each study, taking advantage of its customised expert-based scoring system. The end users involved in the project concluded that CRIBOMICS was easy to learn, use and interact with, reducing the analysis time and possible errors of variant prioritisation for genetic diagnosis.

DONOR-FINDER: A Web Tool for the Automatic Comparison of Genomic Profiles in ART.

The use of genetic tests in assisted reproduction is growing fast. Among potential usages, the selection of the most suitable donor profile stands out. Being able to consider the genomic compatibility between donor and recipient is very important in order to prevent certain diseases. Nevertheless, taking this new factor into account can significantly increase the time needed for donor selection. This paper describes a web-tool designed to automatize the comparison of genomic and phenotypic profiles in assisted reproduction practices, which potentially reduces the chance of error and the time needed in donor-matching processes.