taxonomy

There are 15 repositories under taxonomy topic.

electric-capital / crypto-ecosystems
A taxonomy for open source cryptocurrency, blockchain, and decentralized ecosystems
blockchain crypto-ecosystems cryptocurrency decentralization taxonomy
Language:Rust 1305
MMseqs2
soedinglab / MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
bioinformatics sequence-clustering profile-search sequence-search linclust mmseqs metagenomics alignment blast taxonomy
Language:C 1247
benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
microbiome bioinformatics bioconductor taxonomy amplicon metagenomics metabarcoding
Language:R 446
rinvex / laravel-categories
Rinvex Categorizable is a polymorphic Laravel package, for category management. You can categorize any eloquent model with ease, and utilize the power of Nested Sets, and the awesomeness of Sluggable, and Translatable models out of the box.
php laravel categories taxonomy classification
Language:PHP 445
GTDBTk
Ecogenomics / GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
taxonomy species-assignments phylogenetics archaea bacteria nomenclature bioinformatics metagenomics
Language:Python 426
bugcrowd / vulnerability-rating-taxonomy
Bugcrowd’s baseline priority ratings for common security vulnerabilities
bugcrowd taxonomy vrt vulnerabilities rating
Language:Python 406
shenwei356 / taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
bioinformatics cross-platform lca lineage taxdump taxid taxonkit taxonomy
Language:Go 336
ropensci / taxize
A taxonomic toolbelt for R
taxonomy data api biodiversity biology rstats nomenclature darwincore taxize api-wrapper r r-package
Language:R 262
MISP / misp-taxonomies
Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.
information-exchange classification security taxonomy misp-taxonomies incident-classification government-classification-markings enisa-threat-taxonomy incident-taxonomy incident-response misp-taxonomy machine-tags adversary malware incident
Language:Python 250
bioinformatics-centre / kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
metagenomics next-generation-sequencing bioinformatics taxonomic-classification taxonomy
Language:C 247
OnenoteTaggingKit
WetHat / OnenoteTaggingKit
OneNote (desktop) add-in to manage OneNote pages by page tags
onenote-addin classification facetted-search tagging taxonomy knowledgemanagement
Language:C# 186
widdowquinn / pyani
Application and Python module for average nucleotide identity analyses of microbes.
bioinformatics average-nucleotide-identity taxonomy taxonomy-assignment classification ani
Language:Python 180
wponion
wponion / wponion
~ Lightweight, Flexible & Rapid WP Development Framework ~
wordpress wordpress-theme wordpress-plugin wordpress-plugin-settings wordpress-theme-settings wp-plugin wp-plugin-settings wp-theme-settings wp-theme wp-options wordpress-options-framework wordpress-options-plugin wordpress-options-builder metaboxes metabox settings-api taxonomy user-profile wp wponion
Language:PHP 145
sequana / sequana
Sequana: a set of Snakemake NGS pipelines
ngs variant-calling taxonomy de-novo pacbio sequanix snakemake coverage rna-seq
Language:Jupyter Notebook 140
Nhogs / popoto-examples
Contains a list of Popoto.js examples
cypher northwind taxonomy graph cypher-viewer css-customization query-viewer schema markers region
Language:HTML 139
grunwaldlab / metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
taxonomy metabarcoding trees r community-diversity pcr hierarchical cran
Language:R 132
zyxue / ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
ncbi-taxonomy taxdump lineage python pandas taxonomy ncbi
Language:Python 128
ropensci / rfishbase
R interface to the fishbase.org database
fish fishbase r r-package rstats taxonomy
Language:R 107
AbertayMachineLearningGroup / network-threats-taxonomy
Machine Learning based Intrusion Detection Systems are difficult to evaluate due to a shortage of datasets representing accurately network traffic and their associated threats. In this project we attempt at solving this problem by presenting two taxonomies
security security-tools security-vulnerability security-automation taxonomy network-analysis networking tool hacking hacking-tools research academia
Language:TeX 101
Lecturize / Laravel-Taxonomies
Simple, nestable Terms & Taxonomies (aka Categories) for Laravel.
taxonomy nestable-terms laravel-taxonomies laravel taxonomies categories laravel-category
Language:PHP 94
wp-cli / entity-command
Manage WordPress comments, menus, options, posts, sites, terms, and users.
wp-cli wp-cli-package wordpress cli entity post page user site taxonomy meta option comment menu network term session hacktoberfest
Language:PHP 92
shenwei356 / bio
A lightweight and high-performance bioinformatics package in Golang
bioinformatics golang sequence package syncmer scaled-minhash taxonomy taxdump minimizer
Language:Go 88
sonata-project / SonataClassificationBundle
Symfony SonataClassificationBundle
bundle category php sonata symfony symfony-bundle tag taxonomy
Language:PHP 88
taxonworks
SpeciesFileGroup / taxonworks
Workbench for biodiversity informatics.
species biodiversity-informatics ruby taxonomy biodiversity describe life evolution nomenclature collections
Language:Ruby 81
fideslang
IABTechLab / fideslang
Open-source description language for privacy to declare data types and data behaviors in your tech stack in order to simplify data privacy globally. Supports GDPR, CCPA, LGPD and ISO 19944.
privacy-tools dataprivacy taxonomy open-source privacy-engineering
Language:Python 80
pirovc / ganon
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
metagenomics bioinformatics k-mer bloom-filter microbiome minimizers taxonomy genbank gtdb ncbi refseq
Language:Python 78
mickeysjm / TaxoExpan
The source code used for self-supervised taxonomy expansion method TaxoExpan, published in WWW 2020
graph-neural-network self-supervised-learning taxonomy
Language:Python 74
pr2database / pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
18s-rrna database eukaryotes metabarcoding rrna taxonomy
Language:R 73
morningmoni / TaxoRL
Code for paper "End-to-End Reinforcement Learning for Automatic Taxonomy Induction", ACL 2018
reinforcement-learning dynet taxonomy taxonomy-construction taxonomy-induction wordnet
Language:Python 65
sparna-git / skos-play
SKOS-Play allows to print SKOS files in HTML or PDF. It also embeds xls2rdf to generate RDF from Excel.
d3js rdf semantic-web skos skos-play skos-xl sparql taxonomy thesaurus
Language:Java 64
steineggerlab / Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
bioinformatics k-mer metagenomics taxonomic-classification taxonomy
Language:C++ 62
oisru
oracuk / oisru
Repository for the Open Information Security Risk Universe
risk risk-analysis risk-management taxonomy
Language:Shell 61
maxent-ai / zeroshot_topics
Topic Inference with Zeroshot models
zeroshot-learning nlp machine-learning data-science transformers huggingface keybert bert keyword-extraction nli text-classification labelled-data labelling text weakly-supervised-learning weak-supervision knowledge-graph taxonomy hypernymy-extraction linguistics
Language:Python 60
Imageomics / bioclip
This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral].
clip computer-vision imageomics knowledge-guided-machine-learning taxonomy
Language:Python 58
ArctosDB / arctos
Arctos is a museum collections management system
biodiversity-informatics biodiversity-data biodiversity-standards collections collaboration taxonomy attribution specimen database
Language:ColdFusion 56
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 55