There are 3 repositories under homology topic.
Topological Data Analysis for Python🐍
A Lean Persistent Homology Library for Python
Distances and representations of persistence diagrams
Topological Data Analysis in Python: Simplicial Complex
Flexible and efficient persistent homology computation.
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
Workflow for identifying and classifying homologous gene/protein sequences
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
华中科技大学软件安全课程设计2019
Identification and structural characterization of transcription factors based on supervised machine learning
Topological Data Analysis with Persistent Homology summer course (2021, FGV)
Computing homology groups of simplicial complexes
A simple python project for computing persistent homology
Our implementation of the Smith Normal Form algorithm.
A simple calculator for simplicial homology of finite Delta complexes using Smith normal forms. Final project of MATH 2410: Topology, instructed by Richard Schwartz.
A kmer-based homology searching tool
A bunch of python script and classes to experiment with homology, knot theory and neural networks
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.
Hex on a Voronoi board, using homology to determine game state
ANUBiS is a C++ library of high-performance algorithms for computing topological invariants of point sets and simplicial topological spaces.
Compute persistent homology with coefficients in the field Z/2Z
Magma and GAP methods for working with certain arithmetic groups over imaginary quadratic number fields.
Software for computing the thickness-breadth balls of topological holes from a 3D volumetric object represented by polygonal mesh of its surface.
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.
The repository stores files that are used to determine homology between Mus musculus and Danio rerio genomes by analyzing synteny blocks.
Draw graphs corresponding to double occurrence words and study their properties.
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.
Algorithm I made accompanying my Master's thesis.
Format for efficient storing of homology relations