Algorithm I made accompanying my Master's thesis.
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Updated
Nov 7, 2023 - Python
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
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.
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.
A 2021 Vacation Scholarship project titled "Axiomatic Homology and the Borsuk-Ulam Theorem."
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.
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.
Software for computing the thickness-breadth balls of topological holes from a 3D volumetric object represented by polygonal mesh of its surface.
Topological Data Analysis with Persistent Homology summer course (2021, FGV)
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 Superseded by C++ project "Mackey".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.
Compute the Barcodes of topological spaces
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…
Simple Ripser wrapper in Julia
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