Konstantinos Giatras's repositories
Clustering-Countries-Socioeconomic-Health-Analysis
Exploration and analysis of socio-economic and health data from 167 countries using MATLAB. Application of clustering algorithms to identify development patterns, visualize disparities, and understand global trends.
scRNAseq-Analysis-Pipeline
Comprehensive OOP Python-implemented pipeline for analyzing single-cell RNA-seq data, integrating dimensionality reduction, clustering, and visualization to identify distinct cellular states.
Algorithms-in-Structural-Bioinformatics-Assignments
Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.
Chromosome11-VariantCalling-GATK
A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.
Gastric-Cancer-scRNAseq-Analysis
Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using single‑cell RNA‑seq" by Wang B. et. al, using the raw counts matrix they provide.
Hyperspectral-Image-Clustering
Analysis of the Salinas hyperspectral image dataset using advanced clustering algorithms, focusing on identifying homogeneous regions in the image. Implementations of cost-function optimization and hierarchical clustering techniques, along with evaluations and visualizations in reduced-dimensional spaces.
Image-Processing-and-Analysis-Assignments
Assignments from the 'Image Processing and Analysis' graduate course, focusing on image enhancement techniques and pneumonia detection in chest X-rays using machine learning and deep learning.
INDELseek-Optimized-Implementations
Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other variant callers.
Machine_Learning_Assignments
Machine learning assignments covering regression, classification, neural networks, adversarial examples, and real-time emotion detection using Python. Includes theoretical insights and practical implementations.
ProteinStructurePrediction-ComparativeStudy
Comparison of protein structure prediction methods: Rosetta Ab Initio, which uses fragment assembly, Monte Carlo optimization and energy minimization, and a Linear Algebra Algorithm based on Cayley-Menger matrices.
PTEN-MolecularDynamics-DrugDesign
Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic discovery.
Clustering_Algorithms_Analytical_and_Computational
Analytical and computational exploration of clustering algorithms, focusing on k-means and k-medians, with MATLAB implementations and synthetic dataset analyses.
COVID19-TimeSeries-Forecasting
Modeling and forecasting COVID-19 case trends using time-series data, polynomial regression, and cross-validation for multiple countries.
Diabetes-Prediction-ML-Pipeline
Comprehensive Object-Oriented Programming Python implementation of a machine learning pipeline for diabetes prediction, featuring nested cross-validation, Bayesian hyperparameter optimization, and robust preprocessing for accurate and reliable outcomes.
GiatrasKon
Config files for my GitHub profile.
OverTheWire-Wargames-Solutions
Solutions for OverTheWire wargames, each wargame has its own directory containing Bash scripts for each level's commands.
sandbox.bio-Solutions
Bash scripts replicating the commands from sandbox.bio's interactive bioinformatics tutorials, organized by categories such as Data Exploration, File Formats, Quality Control, and Data Analysis.