schae211

clustree

Visualise Clusterings at Different Resolutions

activitywatch

The best free and open-source automated time tracker. Cross-platform, extensible, privacy-focused.

hdbscan

A high performance implementation of HDBSCAN clustering.

plotnine

A Grammar of Graphics for Python

sleepwalk

Exploring dimension-reduced embeddings

pml2-book

Probabilistic Machine Learning: Advanced Topics

Probabilistic_ML

Material for the "Probabilistic Machine Learning" Course at the University of Tübingen, Summer Term 2023

cs228-notes

Course notes for CS228: Probabilistic Graphical Models.

machine_learning_refined

Notes, examples, and Python demos for the 2nd edition of the textbook "Machine Learning Refined" (published by Cambridge University Press).

obsidiantools

Obsidian tools - a Python package for analysing an Obsidian.md vault

lean4-tactics

Overview of tactics in Lean 4 for beginners — longer version

lean4-cheatsheet

Printable (A4) overview of tactics in Lean 4 for beginners

lean4

Lean 4 programming language and theorem prover

leankernel

jupyter kernel foe lean

mathlib4

The math library of Lean 4

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

dbscan

Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms - R package

root

The official repository for ROOT: analyzing, storing and visualizing big data, scientifically

biodynamo

BioDynaMo is a high-performance and modular, agent-based simulation platform.

Obsidian_to_Anki

Script to add flashcards from text/markdown files to Anki

mojo

The Mojo Programming Language

stringtie

Transcript assembly and quantification for RNA-Seq

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

keyATM

An R package for Keyword Assisted Topic Models

gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

CytoSig

marimo

A reactive notebook for Python — run reproducible experiments, execute as a script, deploy as an app, and version with git.

FLAMEGPU2

FLAME GPU 2 is a GPU accelerated agent based modelling framework for CUDA C++ and Python