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A two-step desktop GUI application for RNA-seq differential gene expression (DEG) analysis. Step 1 reads raw GDC/TCGA STAR gene-count files together with a GDC sample sheet, matches samples to a Tumor/Normal design, and runs PyDESeq2 to produce normalized counts and DEG statistics. Step 2 generates publication-style volcano plots, MA plots, summary bar charts, and expression heatmaps (with optional gene labeling) from the results, exportable as PNG, PDF, SVG, or TIFF. Requires no coding from the user.

A powerful, high-performance bioinformatics framework for discovering, evaluating, and verifying microRNA (miRNA) interactions across DNA, RNA, and protein target sequences. The mirnaprotpred package provides two core modules: SeqFinder: A discovery engine to find all potential miRNA interactions across a genome or target sequence. Validator: A targeted verification engine to test specific, user-provided miRNAs against a target sequence. Both modules are powered by a shared, rigorous biological engine that evaluates exact seed matching, wobble pairing, AU-rich context, and RNAduplex thermodynamic stability.

The Open Neuroscience Graph (openneuroscience.org) is an open-access, curated knowledge graph that maps the open science ecosystem in neuroscience as a browsable digital garden. Built from an Obsidian vault and published as a static website using Quartz, the project replaces traditional linear presentation with a networked structure of interlinked Markdown notes. Bidirectional links, full-text search, and an integrated graph visualization allow users to navigate thematic relationships dynamically rather than sequentially. The complete source material is openly available to sustain, replicate and extend the resource, includding all Markdown content, media attachments, Quartz configuration files, and site customizations. Researchers, educators, and open-science practitioners may explore the site directly, download the vault for offline use in Obsidian, or fork the material to build new, derivative knowledge bases. PID=https://doi.org/10.5281/zenodo.20181900

VigyanLLM is a sovereign, on-premises biomedical AI platform designed for computational biology. It provides autonomous primer design, evaluating melting temperature (Tm) and GC content; CRISPR guide RNA analysis with off-target scoring; BLAST sequence similarity searching; multiple sequence alignment (MSA); and GPU-accelerated molecular docking for drug discovery. Unlike cloud-based SaaS, VigyanLLM deploys via Docker to ensure institutional genomic data sovereignty

edf2csv is a local command-line tool for converting EDF, EDF+, BDF, and BDF+ physiological recordings into CSV and JSON files. It exports signal values, channel information, annotations, and recording metadata while preserving original sampling rates, physical units, and discontinuities.