A 2021 Vacation Scholarship project titled "Axiomatic Homology and the Borsuk-Ulam Theorem."

Algorithm I made accompanying my Master's thesis.

A bunch of python script and classes to experiment with homology, knot theory and neural networks

A kmer-based homology searching tool

Building Pan-Genomes based on Sequence Homology (BPG-SH) constructs and analyzes pan-genomes from multiple organisms. By leveraging sequence homology, BPG-SH integrates genomes to form a comprehensive pan-genome, enhancing our understanding of genetic diversity and evolution.

Homology searcher of Gene Ontologies based on webscrapping and heuristics.

Moja prezentacja o topologicznej analizie danych (chociaż jest bardziej o topologii niż o danych)

Draw graphs corresponding to double occurrence words and study their properties.

Algorithm to parse, assemble and align genomic sequences by use machine learning techniques. The resulting sequences are used to form NCBI-BLAST respects and return sequence homologs.

UDiPH is a package that creates a new metric space where the points are uniformly sampled with respect to a global metric. It is oriented for creating Vietoris-Rips filtrations that are independent of the metric of the initial space.

Implementation of an algorithm to compute persistence homologies

The RO(C4) homology of a point as a Green Functor, and beyond. Superseded by C++ project "Mackey".

A tool to compare protein sequences across UniProt and NCBI RefSeq

Our implementation of the Smith Normal Form algorithm.

LineageHomology uses phylogenies with reconstructed ancestral states to define groups of phylogenetic tips that have gained their states through homologous inheritance or de novo acquisition. LineageHomology can be applied to pathogen phylogeography to define transmission lineages and singletons and derive simple estimates of importation and loc…

Topological Data Analysis with Persistent Homology summer course (2021, FGV)

Software for computing the thickness-breadth balls of topological holes from a 3D volumetric object represented by polygonal mesh of its surface.

The Eilenberg-MacLane Machine (EMM)

A UI build around scikit's ripser module to provide more insight into persistence cohomology.