m-mahgoub

glow

An open-source toolkit for large-scale genomic analysis

quarto-cli

Open-source scientific and technical publishing system built on Pandoc.

python-mammoth

Convert Word documents (.docx files) to HTML

ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

ExplaiNN

ExplaiNN: interpretable and transparent neural networks for genomics

XAI-for-bioinformatics

Explainable AI for Bioinformatics

torch-cam

Class activation maps for your PyTorch models (CAM, Grad-CAM, Grad-CAM++, Smooth Grad-CAM++, Score-CAM, SS-CAM, IS-CAM, XGrad-CAM, Layer-CAM)

Histopathology-Datasets

Ressources of histopathology datasets

puffin

deep learning-inspired explainable sequence model for transcription initiation

plotnine

A Grammar of Graphics for Python

makeyourownneuralnetwork

Code for the Make Your Own Neural Network book

sqlite-utils

Python CLI utility and library for manipulating SQLite databases

FIRE

A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.

bruno

Opensource IDE For Exploring and Testing Api's (lightweight alternative to postman/insomnia)

bootstrap

The most popular HTML, CSS, and JavaScript framework for developing responsive, mobile first projects on the web.

fibertools-rs

Tools for fiberseq data written in rust.

awesome-quarto

A curated list of Quarto talks, tools, examples & articles! Contributions welcome!

nextflow

A DSL for data-driven computational pipelines

rust-bio

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

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

rust-book

The Rust Programming Language: Experimental Edition

flask-on-docker

Flask + Docker

rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

nf-core-hic

Pipeline for Hi-C data analysis

nf-core-wgsnano

Nextflow pipeline for analysis of Nanopore Whole Genome Sequencing

book

sgkit

Scalable genetics toolkit

TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.

cutnrun

nf-core-chipseqcr

Nextflow pipeline for ChIP-seq and CUT&RUN analysis based on an nf-core template