Loukas Theodosiou

cnsplots. 🎨 Toolkit for generating publication-quality plots for Cell, Nature and Science journals

line. tiny command-line midi sequencer and language for live coding music

DEGgo. Differential Expression and Gene Ontology enrichment analysis for bulk RNA-seq data

ltc-color-palettes. "ltc_palettes: Tailored for data visualization enthusiasts, ltc_palettes is an R package that offers a curated collection of color palettes. Crafted to enhance clarity and impact, these palettes ensure that your visual representations not only communicate data effectively but also aesthetically

BioinformaticiansToolbox. Training materials for all things bioinformatics

mafsmith. Fast, self-contained VCF to MAF converter with embedded annotation (Rust rewrite of vcf2maf)

ML-Course-Notes. 🎓 Sharing machine learning course / lecture notes.

world-cup-prediction-py. Python

Machine-Learning. Assorted ML tutorials that I originally wrote for Decoding Biology

ai_book. Supporting code for Welch Labs AI Book

world-cup-predictor. Python

nucleotide-transformer. Foundation Models for Genomics & Transcriptomics

Awesome-AI-Meets-Biology. Awesome-AI-Meets-Biology is a collection of state-of-the-art, novel, exciting LLMs and agents on biomedical and bioinformatic fields.

DnaFeaturesViewer. :eye: Python library to plot DNA sequence features (e.g. from Genbank files)

science-skills. GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools.

DeepFRI. Deep functional residue identification

eurolig. R package for obtaining and analyzing basketball data from the Euroleague

world-press-freedom-2026. Source code for the story on the 2026 RSF World Press Freedom Ranking

CompareM. A toolbox for comparative genomics.

RuVector. RuVector is a High Performance, Real-Time, Self-Learning Ai, Vector GNN, Memory DB built in Rust.

ggvolc. 𝐠𝐠𝐯𝐨𝐥𝐜 effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unprecedented ease. With just a single line of code, visualize complex datasets, gaining deeper insights and simplifying data representation

mempalace. The best-benchmarked open-source AI memory system. And it's free.

ade-python. Python library for Agentic Document Extraction (ADE).

GLM-OCR. GLM-OCR: Accurate × Fast × Comprehensive

genes_synteny. This repository contains a tutorial and scripts to create a gene synteny and homology figure for a set of species.

Synteny-Tutorial. Shell

NetGP. Python

SciencePlots. Matplotlib styles for scientific plotting

gReLU. gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

minAlphaFold2. A minimal PyTorch re-implementation of AlphaFold2's model & training

PlantBioinformatics. Materials of the course WBIO-A-08 Plant Bioinformatics

beyond-tax-haven. Code repo of the paper Beyond the Tax Haven: A Graph Analysis of Business Attraction in Swiss Municipalities

intro-machine-learning-training. Jupyter Notebook

machine_learning. Machine learning in R

OpenCRISPR. AI-generated gene editing systems

antifp2. Prediction of anti-fungal proteins using protein language models

superpowers. An agentic skills framework & software development methodology that works.

ggupset. Combination matrix axis for 'ggplot2' to create 'UpSet' plots

ggincerta. R

scientific-agent-skills. Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 170,000+ scientists worldwide. 158 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.

claude-code-templates. CLI tool for configuring and monitoring Claude Code

ml-from-omics. Code required to reproduce results from the book chapter "Machine learning from omics data" (Springer Protocols, 2021)

ggbot2. R

PANICLE. Python package for Genome-Wide Association Studies (GWAS). Implements GLM, MLM, FarmCPU, and BLINK with support for VCF, PLINK, HapMap, and CSV genotype formats.

ggregions. R

CellVoyager. Python

ISCB20.09. Introduction to R

LongReadGenotyping. GENOCAP (GENOtyping by long-read target CAPture) pipeline

gcb-2025-scripts-to-pipeline. This holds all files related to the workshop "From a Collection of Scripts to a Pipeline – Writing Nextflow Workflows with nf-core Best Practices" at the GCB 2025.

snvstory. Rapid and accurate ancestry inference using SNVs.

applied-computational-genomics. Applied Computational Genomics Course at UU: Spring 2020

Bioinformatics_Toolkit. A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

GPro. GPro: a toolbox for Generative approaches in promoter design

DeepCRE. Deep learning the cis-regulatory code for gene expression in selected model plants

fetchngs. Pipeline to fetch metadata and raw FastQ files from public databases

data-viz-resources. Resources relating to data visualisation.

cookiecutter. A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.

gemini-cli. An open-source AI agent that brings the power of Gemini directly into your terminal.

PAINTOR_V3.0. Fast, integrative fine mapping with functional data

merizo_search. Fast protein domain structure embedding+search tool

vcf2gwas. Python API for comprehensive GWAS analysis using GEMMA

phylogram_d3. Interactive phylogenetic tree based on D3.js

TOGA. TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

omnifluss. Computational workflow for virus genome reconstruction

tsinfer. Infer population size and selection coefficient from time-series allele-frequency data

seqrush. online variation graph induction

anvio. An analysis and visualization platform for 'omics data

dso. Data Science Operations (dso) command line tool

fastML. A Python package built on sklearn for running a series of classification Algorithms in a faster and easier way.

GeneSelectR_benchmarking. R

KnnSleepwalk. R package that allows for visualization of the KNN of an embedding compared to the KNN of the original high-dimensional data.

Machine-Learning-Workflow-with-Python. This is a comprehensive ML techniques with python: Define the Problem- Specify Inputs & Outputs- Data Collection- Exploratory data analysis -Data Preprocessing- Model Design- Training- Evaluation

Read2Ring. A simple bash-based pipeline to generate Krona charts from SRA accessions using Kraken2.

applied-bioinformatics-thesis. Exploring Machine Learning Algorithms on mRNA Expression Data of Rheumatoid Arthritis

goPredSim. Python

MCScanX. MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

bayesplot. bayesplot R package for plotting Bayesian models

Physalia_MLOmicsIntegration_2025. Physalia course Machine Learning for Multi-Omics Integration

pal-mcp-server. The power of Claude Code / GeminiCLI / CodexCLI + [Gemini / OpenAI / OpenRouter / Azure / Grok / Ollama / Custom Model / All Of The Above] working as one.

TWAStutorial. This tutorial is a guide to perform TWAS with the data used in Torres‐Rodríguez, J. Vladimir, et al. "Population‐level gene expression can repeatedly link genes to functions in maize." The Plant Journal (2024).

book-mapping-worlds-with-r-examples. You will find all the scripts organized by chapter of my book "Mapping Worlds with R: Your Journey from Beginner to Data Cartographer" in this GitHub repo.

euro2025. R

SpatialEffects. R

gradio. Build and share delightful machine learning apps, all in Python. 🌟 Star to support our work!

Organic-Indicator. In this project, we explored the features of potential consumers for organic products by analyzing grocery sales data.

kaggle-nlp-sarcastic-tweets. https://www.kaggle.com/c/nlp-getting-started kaggle comp submission!

svelteplot. Svelte-native plotting framework based on the grammar of graphics

TargetGenes. This code was my final assignment within my MBINF program. Here I have used python to take raw rnaSeq data and utilize machine learning methods along with PCA to identify lists of genes that may be targeted by the Wnt signaling pathway.

Xgboost-for-scRNAseq. A workflow for applying tree-based machine learning algorithms such as Random forest and Xgboost to scRNAseq data

MachineLearningRNASeq. Machine Learning Algorithms for Cancer Sample Prediction

RNAseq_titration_results. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

ConsensusML. Machine Learning to Detect Cancer Biomarkers from RNAseq Data

mcptools. Model Context Protocol For R

TabPFN. ⚡ TabPFN: Foundation Model for Tabular Data ⚡

learning_shiny. Learning about Shiny

2025_f1_predictions. Python

RKaggle. An R package for downloading datasets from Kaggle into the R Console

Terrorism_Analysis. This is a StrataScratch exercise, whose aim is to analyze the terrorism activity between 1970 to 2017. Check the link in the notebook for all the details.

Season3_Episode10. My Kaggle challenge attempt for S3_E10. In this case I wanted to try LazyPredict and CalibratedClassifierCV.

lime. Lime: Explaining the predictions of any machine learning classifier

ml_dashboard_streamlit. ML Dashboard using Streamlit

MIL-Manim. Multiple Instance Learning Animations with Manim.

streamlit_ml_dashboard. Dashboard to Tune Hyperparameters of ML Model

ml_animated. Use animation to explain machine learning

severance-reddit. R

meta-analysis_egg_hormones_and_fitness. This is a repository that contains all code and data needed to reproduce the results of a meta-analytic study on the relationship between egg hormones and fitness proxies across bird species

user2024-tutorial-gswep. useR! 2024 Tutorial Slides: Good Software Engineering Practice for R Packages

2024_Habich_et_al. R

VoronoiPlus. Create weighted Voronoi maps and treemaps

Quick_data_vis. Introduction to data visualization with R

TidyLocalSynteny. A Tidyverse-based workflow for local synteny visualization

cleanlab. Cleanlab's open-source library is the standard data-centric AI package for data quality and machine learning with messy, real-world data and labels.

tinytable. Simple and Customizable Tables in `R`

fastcov. For when you just need a coverage plot.

CoVpipe2. SARS-CoV-2 genome reconstruction for Illumina data in Nextflow

national-highways. R package for accessing the National Highways WebTRIS API via R.

dkb-robo. library to access the internet banking area of "Deutsche Kreditbank" to get account information and transactions

ggtext. Improved text rendering support for ggplot2

RNA-seq. Step-by-step analysis pipeline for RNA-seq data

scripts_grad_school. Scripts created during grad school

plot-VCF. visual analysis of your VCF files

Conference-app. Code for generating a web app to visualise the program of SORTEE conferences.

trackplot. Generate IGV style locus tracks from bigWig files in R

gh_actions_test. R

parquetize. R package that allows to convert databases of different formats to parquet format

ggalign. Integrative Composable Visualization Framework for ggplot2

How-to-Create-Circular-Graphs-in-R. This tutorial condenses the `circlize` manual for creating circular graphs in R

mofa-workshop. Jupyter Notebook

euroleaguer. euroleaguer provides an easy way to retrieve data from EuroLeague and EuroCup API with R. This is an un-official API wrapper and we recommend to follow usual rules of conduct when dealing with open API calls.

euroleaguer. :exclamation: This is a read-only mirror of the CRAN R package repository. euroleaguer — 'Euroleague basketball API'. Homepage: https://github.com/FlavioLeccese92/euroleaguer/

awesome_spatial_omics. tools and notes for spatial omics

astgrepr. Parse and Manipulate R Code

VR-data-tools. R scripts for analysing VR headset production related data.

superheat. An r package for generating beautiful and customizable heatmaps

euroleague_api. A python package for the Euroleague API

soccerAnimate. R package to create 2D animations of soccer tracking data in addition to calculate stats for both team and player level

netflix-app. A Movie Recommender App

BAMdash. create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

pyRforest. pyRforest: A comprehensive R package for genomic data analysis featuring scikit-learn Random Forests in R

math_for_compbio. This repository contains math tutorials I created for Bioinformatics and Computational Biology.

tidyCoverage. R

mapro. Marker discovery in prokaryotes

PopGenScripts. Python

Euro2024_data.

R2D2. Reconstructing RNA Dynamics from Data

geneviewer. An R package designed for drawing gene arrow maps

vgp. analysis sketches for vertebrate genomes project assemblies

Machine-Learning-with-R-datasets. Formatted datasets for Machine Learning With R by Brett Lantz

SandFlyComparativeGenomics. Source code for the manuscript of Charamis et al. (2024)

cellxgene_VIP. Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

scrnaseq. Single cell RNA sequencing

fastqc-docker. Simple container for Fastqc

google-research. Google Research

100-Days-Of-ML-Code. 100 Days of ML Coding

getting-started-with-genomics-tools-and-resources. Unix, R and python tools for genomics and data science

ggentropy. A cross platform entropy library

conf-talk-2023. SCSS

ttmeta. TidyTuesday Dataset Metadata

dockerdemo. Example dockerfiles for plumber, shiny, and quarto

ggmagnify. Create a magnified inset of part of a ggplot object

awesome-public-real-time-datasets. A list of publicly available datasets with real-time data maintained by the team at bytewax.io

Rscripts. R

rconnection. Writing a custom connection for R

Monocypher. An easy to use, easy to deploy crypto library

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

dataviz-nc3. R

random-data-viz. Random data visualizations

tidyseurat. Seurat meets tidyverse. The best of both worlds.

MicrobiomeBestPracticeReview. Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

chromsyn. Chromosome-level synteny plotting using orthologous regions

multiGenomicContext. multiGenomicContext is a pipeline to see your protein in many genomic context as much as gbk you have.

GGisy. Genome-Genome circle synteny

gggenes. ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

GENESPACE. R

ggtree. :christmas_tree:Visualization and annotation of phylogenetic trees

seqvisr. Biological sequence visualization functions in R

drawProteins. Creating package to draw proteins from Uniprot API

numbat. Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

physalia_adaptation_course.

awesome-genome-visualization. A list of interesting genome browser and genome visualization programs

minipileup. Simple pileup-based variant caller

Edition2025.

impg. implicit pangenome graph

RIdeogram. R

physalia_adaptation_course. R

rstudio-conf. Materials for rstudio::conf

new_app. TypeScript

web-scraping. R

tidychatmodels. Chat With All Kinds of AI Models Through a Common Interface

tidytuesday. My contributions to the #TidyTuesday challenge

metaseqr2-tutorial. R

rnaseq. RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

ChessGMsdata. This R package offers a comprehensive dataset on chess grand masters.

Phylogeny-project. All the scripts I wrote as part of THE BIOL0019 Advanced Research Project assignment

single-cell-best-practices. https://www.sc-best-practices.org

crowdsourcing. R

phylophysalia2023. Python

shiny_examples. Examples of Shiny applications. Examples vary in terms of plots, functionality, and complexity. Multiple examples are provided for plots for educational pruposes.

football-match-predictor. A machine learning project that predicts results of a football match

ggkegg. Analyzing and visualizing KEGG information using the grammar of graphics