A list of software for pangenomics
VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications. Users simply provide a directory with output files and VueGen compiles them into a structured report.
splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.
Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation
High-performance Julia tool for sequence demultiplexing
A searchable catalog of cfDNA tools for WGS, methylation, CNA, end motif, coverage, and tissue-origin workflows.
Batch Effect Correction framework for metagenomic data
Python package for creating interactive and static visualizations of multi-omics data
Easy Way to Generate PSSM from the FASTA Sequences
State-of-the-art biology program translation pipeline and scheduler
EpiRNA-Scanner, a publicly deployed web framework that processes sequences from 41 bases to over 100,000 bases without manual preprocessing. The system introduces Epitranscriptomic Boundary Contrast Scoring (EBCS), producing single-nucleotide resolution predictions anchored to degenerate DRACH motifs.
Bioinformatics Dependencies Platform - A better way to manage your bioinformatics data sources, search and query across multiple bioinformatics databases, tooling. Properly version and reproduce your research, generate citation and data acessibility statement.
BioGenie is a complete bioinformatics command line tool, written in C++.
DNA mutation clustering tool for fast detection of likely false-negative DNA variants and likely related mutants in a sequenced population of independently mutagenized individuals. Other uses include analysis of segregating mutants and the detection of problematic samples in a sequenced population.
A powerful cladogram making software, made to create cladograms, phenograms, and chronograms !
EDAMannot is a command-line toolbox which applies to annotations related to the EDAM ontology.
Gene editing, protein design, and project management — all in one place, all on your machine.
MethScope: Cloud-Native Interactive Genome Browser for Nanopore DNA Methylation
A pathway‑centric classification strategy for robust and platform‑independent molecular subtyping of head and neck squamous cell carcinoma
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