A Lean Persistent Homology Library for Python
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Updated
Sep 23, 2024 - C++
A Lean Persistent Homology Library for Python
Topological Data Analysis for Python🐍
Distances and representations of persistence diagrams
Use Thor's Axe to cut exons into their evolutionary building blocks ⚡
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
Flexible and efficient persistent homology computation.
Draw graphs corresponding to double occurrence words and study their properties.
Computes polyhedral fundamental domains and homology of the moduli space of unlabeled networks on n vertices. Generalizes to polyhedral region X, finite group G with linear action.
Algorithm I made accompanying my Master's thesis.
Software for computing the thickness-breadth balls of topological holes from a 3D volumetric object represented by polygonal mesh of its surface.
Functional annotation transfer tool in Golang.
A simple calculator for simplicial homology of finite Delta complexes using Smith normal forms. Final project of MATH 2410: Topology, instructed by Richard Schwartz.
Computing homology groups of simplicial complexes
Workflow for identifying and classifying homologous gene/protein sequences
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.
A simple python project for computing persistent homology
A kmer-based homology searching tool
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.
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…
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