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Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.

Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.

Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets.

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)

A quality control tool for high throughput sequence data.

Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.

CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)