homology

There are 3 repositories under homology topic.

scikit-tda / scikit-tda
Topological Data Analysis for Python🐍
homology mapper scikit-tda tda tda-libraries tda-python topological-data-analysis topology
Language:Python 492
scikit-tda / ripser.py
A Lean Persistent Homology Library for Python
topological-data-analysis persistent-homology homology topology tda data-science ripser
Language:C++ 259
scikit-tda / persim
Distances and representations of persistence diagrams
persistence-images topology homology tda bottleneck-distance persistence-image python sliced-wasserstein-distance persistence-diagrams
Language:Python 120
stephenhky / MoguTDA
Topological Data Analysis in Python: Simplicial Complex
tda python package topology homology topological-data-analysis
Language:Python 110
Ripserer.jl
mtsch / Ripserer.jl
Flexible and efficient persistent homology computation.
persistent-homology topological-data-analysis homology cohomology tda ripser julia topology
Language:Julia 59
gheber / kenzo
A repackaged version of the Kenzo program by Francis Sergeraert and collaborators.
homology computation lisp algebraic-topology
Language:Common Lisp 50
r2g
yangwu91 / r2g
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
bioinformatics ncbi-sra homology orthology bioinformatics-pipeline phylogenetics gene-sequence-retrieval
Language:Python 49
rrrlw / TDAstats
R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
topological-data-analysis homology-calculations cran ripser ggplot2 pipeline r persistent-homology tda homology topology homology-computation visualization data-science r-package joss r-packages topology-visualization
Language:R 35
laelbarlow / amoebae
Workflow for identifying and classifying homologous gene/protein sequences
bioinformatics hmmer3 biopython python3 blast genome-annotation similarity-search coulson-plot transcriptome-annotation snakemake-workflow comparative-genomics homology molecular-evolution gene-families protein-families orthology
Language:Python 17
PhyloSofS-Team / thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
bioinformatics alternative-splicing protein-evolution exon homology orthology-inference
Language:Python 10
glarue / reciprologs
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
orthologs orthology-inference bioinformatics homology
Language:Python 9
BIONF / HaMStR
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
homology homology-search orthology-inference orthology
Language:Perl 8
mtsch / Ripser.jl
Simple Ripser wrapper in Julia
julia tda homology topological-data-analysis computational-topology persistent-homology
Language:Julia 8
smu160 / Persistent-Homology
python topology homology visualization
Language:Python 7
Billy1900 / Homology-AND-CFG-Detection
华中科技大学软件安全课程设计2019
cfg cfg-rules format-string-attack homology integer-overflow integer-width stackoverflow
Language:Python 6
lucasresck / topological-data-analysis
Topological Data Analysis with Persistent Homology summer course (2021, FGV)
topology topological-data-analysis homology
Language:Jupyter Notebook 6
Pseudomanifold / CompHom
Computing homology groups of simplicial complexes
homology-computation c-plus-plus simplicial-complexes manifolds simplicial-homology homology algebraic-topology
Language:C++ 6
draeger-lab / TFpredict
Identification and structural characterization of transcription factors based on supervised machine learning
machine-learning bioinformatics transcription-factor prediction homology blast transcription-factors fasta identification sabine
Language:Java 5
dzinghan / smith-normal-form-calculator
Our implementation of the Smith Normal Form algorithm.
python linear-algebra matrix homology similarity smith-normal-form sympy
Language:Python 3
maroon-scorch / Computational-Homology
A simple calculator for simplicial homology of finite Delta complexes using Smith normal forms. Final project of MATH 2410: Topology, instructed by Richard Schwartz.
homology topological-data-analysis topology
Language:Python 3
Quenouillaume / persil
A simple python project for computing persistent homology
homology rips-complex persistence-diagram
Language:Python 3
aclemen1 / EMM
The Eilenberg-MacLane Machine (EMM)
homology homotopy eilenberg-maclane
Language:C++ 2
alex-louvet / nnexpy
A bunch of python script and classes to experiment with homology, knot theory and neural networks
nnexpy homology nn-expressiveness knots
Language:Python 2
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.
filtration homology machine-learning simplicial-complex topological-data-analysis
Language:Python 2
nasosev / voronoi-hex
Hex on a Voronoi board, using homology to determine game state
board-game homology
Language:Python 2
KmerGMA.jl
Qile0317 / KmerGMA.jl
A kmer-based homology searching tool
bioinformatics genomics homology homology-search kmer kmer-counting
Language:Julia 2
ANUBiS
jmaerte / ANUBiS
ANUBiS is a C++ library of high-performance algorithms for computing topological invariants of point sets and simplicial topological spaces.
topological-data-analysis topological-data-structures homology homology-computation homology-calculations simplicial-complexes smith-normal-form topology
Language:C++ 1
MB-29 / topological_persistence
Compute persistent homology with coefficients in the field Z/2Z
topological-data-analysis barcode filtrations homology topology data tda persistence diagram persistence-diagram python3
Language:Python 1
schoennenbeck / VMH-ImaginaryQuadraticNumberFields
Magma and GAP methods for working with certain arithmetic groups over imaginary quadratic number fields.
magma number-theory gap arithmetic-groups numberfield homology
Language:GAP 1
Yann-Situ / Hole-Measures
Software for computing the thickness-breadth balls of topological holes from a 3D volumetric object represented by polygonal mesh of its surface.
algebraic-topology holes homology homology-computation computer-aided-design geometry-computation
Language:C++ 1
Alepidoptera7 / assembly_scaffold_BLAST
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.
alignment-algorithm bioinformatics-pipeline biopython de-novo-assembly graph-theory-algorithms homology machine-learning philogenetic-trees
Language:Python 0
dansta0804 / Tbx5_analysis_II
The repository stores files that are used to determine homology between Mus musculus and Danio rerio genomes by analyzing synteny blocks.
chip-seq danio-rerio r regeneration tbx5 circos-plot mus-musculus synteny-block cinteny symap homology
Language:HTML 0
fajardogomez / dowgraphs
Draw graphs corresponding to double occurrence words and study their properties.
directed-graphs homology
Language:Python 0
iamaizhan / BPG-SH
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.
bioinformatics bioinformatics-pipeline homology pan-genome
0
xalhs / reciprocity-formulas
Algorithm I made accompanying my Master's thesis.
algebraic-topology group-theory cokernel gauss-sum linking-form linking-matrix reciprocity-formula homology free-homology torsion-homology
Language:Python 0
gaojunxuan / homology_storage_compara
Format for efficient storing of homology relations
bioinformatics data-structures homology phylogenetic-trees
Language:C++

homology

scikit-tda / scikit-tda

scikit-tda / ripser.py

scikit-tda / persim

stephenhky / MoguTDA

mtsch / Ripserer.jl

gheber / kenzo

yangwu91 / r2g

rrrlw / TDAstats

laelbarlow / amoebae

PhyloSofS-Team / thoraxe

glarue / reciprologs

BIONF / HaMStR

mtsch / Ripser.jl

smu160 / Persistent-Homology

Billy1900 / Homology-AND-CFG-Detection

lucasresck / topological-data-analysis

Pseudomanifold / CompHom

draeger-lab / TFpredict

dzinghan / smith-normal-form-calculator

maroon-scorch / Computational-Homology

Quenouillaume / persil

aclemen1 / EMM

alex-louvet / nnexpy

antonio-leitao / udiph

nasosev / voronoi-hex

Qile0317 / KmerGMA.jl

jmaerte / ANUBiS

MB-29 / topological_persistence

schoennenbeck / VMH-ImaginaryQuadraticNumberFields

Yann-Situ / Hole-Measures

Alepidoptera7 / assembly_scaffold_BLAST

dansta0804 / Tbx5_analysis_II

fajardogomez / dowgraphs

iamaizhan / BPG-SH

xalhs / reciprocity-formulas

gaojunxuan / homology_storage_compara