Bramble: genome to transcriptome coordinate conversion 🌿🫐

Emending Alignment of Spliced Transcript Reads

A tool for projecting genomic alignments to transcriptomic coordinates

A small database of weird gene annotations

Iterate over minimizers of a DNA sequence

A very fast interval tree data structure

cool BED-to-GFF3 converter that runs in parallel

Bootstrap 4 stylesheet that implements vertically-oriented navigation tabs.

😠 UpSet.js - a set visualization library for rendering UpSet Plots (a JavaScript re-implementation of UpSet(R) by Lex et al), Euler Diagrams, Venn Diagrams, and Karnaugh Maps

Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.

DTU analysis tool inspired by llamas

Dragon distributed runtime for HPC and AI applications and workflows

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

A Rust library for building modular, fast and compact indexes over genomic data

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

Transcript clustering

The Monorepo for Runestone Academy servers and interactives

Foreign DNA/RNA integration site detection

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust.

Ultra-efficient and sensitive method to search for Open Reading Frames in spliced genomes guided by reference annotation to maximize protein similarity within genes.

Small independent tracker for the JHU transloc services to keep count of the missed shuttles and the total lateness each day

Joyplots in Python with matplotlib & pandas 📈

GCLib - Genomic C++ library of reusable code for bioinformatics projects

Various small scripts and tools written in various languages to help in genomic analysis

Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/