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homology

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scikit-tda /scikit-tda

Topological Data Analysis for Python🐍

topology mapper topological-data-analysis tda homology scikit-tda tda-python tda-libraries

UpdatedJul 19, 2024
Python

scikit-tda /ripser.py

A Lean Persistent Homology Library for Python

data-science topology persistent-homology topological-data-analysis tda homology ripser

UpdatedMar 17, 2025
C++

scikit-tda /persim

Distances and representations of persistence diagrams

python topology tda persistence-diagrams homology persistence-images sliced-wasserstein-distance bottleneck-distance persistence-image

UpdatedMar 12, 2025
Python

stephenhky /MoguTDA

Topological Data Analysis in Python: Simplicial Complex

python package topology topological-data-analysis tda homology

UpdatedMar 17, 2025
Python

Ripserer.jl

mtsch /Ripserer.jl

Flexible and efficient persistent homology computation.

topology julia persistent-homology topological-data-analysis tda homology ripser cohomology

UpdatedDec 19, 2024
Julia

gheber /kenzo

A repackaged version of the Kenzo program by Francis Sergeraert and collaborators.

lisp computation algebraic-topology homology

UpdatedFeb 6, 2025
Common Lisp

r2g

yangwu91 /r2g

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval

UpdatedApr 2, 2021
Python

rrrlw /TDAstats

R pipeline for computing persistent homology in topological data analysis. Seehttps://doi.org/10.21105/joss.00860 for more details.

visualization data-science ggplot2 cran r topology pipeline r-package joss persistent-homology topological-data-analysis tda homology ripser r-packages homology-computation homology-calculations topology-visualization

UpdatedNov 23, 2021
R

laelbarlow /amoebae

Workflow for identifying and classifying homologous gene/protein sequences

bioinformatics python3 biopython gene-families genome-annotation blast comparative-genomics molecular-evolution similarity-search protein-families orthology homology snakemake-workflow hmmer3 transcriptome-annotation coulson-plot

UpdatedJan 16, 2025
Python

glarue /reciprologs

Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.

bioinformatics orthology-inference orthologs homology

UpdatedJun 6, 2024
Python

PhyloSofS-Team /thoraxe

Use Thor's Axe to cut exons into their evolutionary building blocks ⚡

bioinformatics alternative-splicing orthology-inference exon protein-evolution homology

UpdatedJun 14, 2024
Python

BIONF /HaMStR

Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.

orthology-inference homology-search orthology homology

UpdatedOct 6, 2020
Perl

lucasresck /topological-data-analysis

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

topology topological-data-analysis homology

UpdatedFeb 14, 2021
Jupyter Notebook

mtsch /Ripser.jl

Simple Ripser wrapper in Julia

julia persistent-homology topological-data-analysis tda computational-topology homology

UpdatedJun 3, 2020
Julia

smu160 /Persistent-Homology

visualization python topology homology

UpdatedMay 7, 2019
Python

draeger-lab /TFpredict

Identification and structural characterization of transcription factors based on supervised machine learning

machine-learning bioinformatics transcription-factors prediction identification fasta blast transcription-factor homology sabine

UpdatedJan 24, 2025
Java

Pseudomanifold /CompHom

Computing homology groups of simplicial complexes

c-plus-plus simplicial-complexes algebraic-topology manifolds homology homology-computation simplicial-homology

UpdatedJul 20, 2023
C++

Quenouillaume /persil

A simple python project for computing persistent homology

homology persistence-diagram rips-complex

UpdatedMay 5, 2023
Python

antonio-leitao /udiph

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.

machine-learning topological-data-analysis filtration homology simplicial-complex

UpdatedJan 12, 2022
Python

KmerGMA.jl

Qile0317 /KmerGMA.jl

A seed-based homology searching tool

bioinformatics genomics kmer homology-search kmer-counting homology

UpdatedApr 24, 2023
Julia

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