bioinformatics

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlation...

A tutorial on methods of 16S analysis with QIIME 1

A modern genomics framework for julia

Bayesian MCMC matrix factorization algorithm

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a...

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

Horizontal gene transfer (HGT) identification pipeline

From annotated genomes to metabolic screening in large scale microbiotas

Statistical approach for removing unwanted variation from multiple single-cell datasets

Exon is an OLAP query engine specifically for biology and life science applications.

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Butler is a framework for running scientific workflows on public and academic clouds.

Bonsai: Fast, flexible taxonomic analysis and classification

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Arioc: GPU-accelerated DNA short-read alignment

BISulfite-seq CUI Toolkit

Rust implementation of a fast, easy, interval tree library nim-lapper

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Efficiently read and write sequencing data from Python

A Nextflow workflow to generate lift over files for any pair of genomes

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools....

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

Thermo MSFileReader Python bindings

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone...

Genomics data visualization in Python by using matplotlib.

:golf: GO-terms Semantic Similarity Measures

vembrane filters VCF records using python expressions

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention...

Elucidating the Utility of Genomic Elements with Neural Nets

𝐠𝐠𝐯𝐨𝐥𝐜 effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unpre...

Node.js module for working with the NCBI API (aka e-utils).

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Analysis of non-covalent interactions in MD trajectories

Collects software dedicated to predicting specific properties of peptides

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-ti...

SplitThreader has moved into Ribbon!

Mulled - Automatized Containerized Software Repository

Protein structure comparison tools such as SSAP and SNAP

A Python library to visualize and analyze long-read transcriptomes

R Package Illustrating Components of an R package for BCB410H - Applied Bioinformatics (2019-2025), University of Toronto, Canada

Python package to annotate and visualize gene fusions.

Fast FASTQ sample demultiplexing in Rust.

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Core library of the Genome Analysis Toolbox with de-Bruijn graph

API for linked biological knowledge

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

A geometric deep learning framework (Geometric Transformers) for predicting protein interface contacts. (ICLR 2022)

Detecting methylation using signal-level features from Nanopore sequencing reads of plants