taxonomy | Topic | Ecosyste.ms: Repos

Topic: "taxonomy"

electric-capital/crypto-ecosystems

A taxonomy for open source cryptocurrency, blockchain, and decentralized ecosystems

Language: Zig - Size: 176 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1,747 - Forks: 1,584

soedinglab/MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

Language: C - Size: 30.6 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 1,660 - Forks: 223

Ecogenomics/GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Language: Python - Size: 28.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 517 - Forks: 84

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

Language: R - Size: 468 MB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 495 - Forks: 148

bugcrowd/vulnerability-rating-taxonomy

Bugcrowd’s baseline priority ratings for common security vulnerabilities

Language: Python - Size: 572 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 475 - Forks: 92

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.

Language: PHP - Size: 346 KB - Last synced at: 9 days ago - Pushed at: almost 2 years ago - Stars: 469 - Forks: 71

shenwei356/taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Language: Go - Size: 14.2 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 412 - Forks: 32

ropensci/taxize

A taxonomic toolbelt for R

Language: R - Size: 36.6 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 279 - Forks: 62

bioinformatics-centre/kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Language: C - Size: 906 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 278 - Forks: 67

MISP/misp-taxonomies

Taxonomies used in MISP taxonomy system and can be used by other information sharing tool.

Language: Python - Size: 3.68 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 276 - Forks: 141

widdowquinn/pyani

Application and Python module for average nucleotide identity analyses of microbes.

Language: Python - Size: 185 MB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 208 - Forks: 57

Imageomics/bioclip

This is the repository for the BioCLIP model and the TreeOfLife-10M dataset [CVPR'24 Oral, Best Student Paper].

Language: Python - Size: 28.9 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 202 - Forks: 20

WetHat/OnenoteTaggingKit

OneNote (desktop) add-in to manage OneNote pages by page tags

Language: C# - Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 177 - Forks: 15

Nhogs/popoto-examples

Contains a list of Popoto.js examples

Language: HTML - Size: 8.24 MB - Last synced at: 2 days ago - Pushed at: 7 months ago - Stars: 148 - Forks: 54

wponion/wponion

~ Lightweight, Flexible & Rapid WP Development Framework ~

Language: PHP - Size: 20.6 MB - Last synced at: 7 days ago - Pushed at: almost 4 years ago - Stars: 147 - Forks: 19

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.8 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 146 - Forks: 28

zyxue/ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

Language: Python - Size: 395 KB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 145 - Forks: 30

grunwaldlab/metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

Language: R - Size: 107 MB - Last synced at: 9 days ago - Pushed at: 4 months ago - Stars: 140 - Forks: 29

steineggerlab/Metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Language: C++ - Size: 92.4 MB - Last synced at: 6 days ago - Pushed at: 9 days ago - Stars: 139 - Forks: 12

ropensci/rfishbase

R interface to the fishbase.org database

Language: R - Size: 265 MB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 117 - Forks: 42

SpeciesFileGroup/taxonworks

Workbench for biodiversity informatics.

Language: Ruby - Size: 97.8 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 102 - Forks: 30

wp-cli/entity-command

Manage WordPress comments, menus, options, posts, sites, terms, and users.

Language: PHP - Size: 8.88 MB - Last synced at: 3 days ago - Pushed at: 12 days ago - Stars: 101 - Forks: 95

Lecturize/Laravel-Taxonomies

Simple, nestable Terms & Taxonomies (aka Categories) for Laravel.

Language: PHP - Size: 155 KB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 99 - Forks: 30

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

Language: TeX - Size: 864 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 98 - Forks: 24

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

Language: Python - Size: 24.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 96 - Forks: 12

shenwei356/bio

A lightweight and high-performance bioinformatics package in Golang

Language: Go - Size: 1.86 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 93 - Forks: 9

sonata-project/SonataClassificationBundle

Symfony SonataClassificationBundle

Language: PHP - Size: 1.61 MB - Last synced at: 1 day ago - Pushed at: 15 days ago - Stars: 91 - Forks: 112

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.

Language: Python - Size: 1.45 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 88 - Forks: 12

moshi4/ANIclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

Language: Python - Size: 184 MB - Last synced at: 7 days ago - Pushed at: 29 days ago - Stars: 80 - Forks: 10

pr2database/pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

Language: R - Size: 761 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 80 - Forks: 7

wikibonsai/wikibonsai

A jungle gym for thought with an API for the mind.

Language: Svelte - Size: 37.8 MB - Last synced at: 12 days ago - Pushed at: 5 months ago - Stars: 79 - Forks: 3

mickeysjm/TaxoExpan

The source code used for self-supervised taxonomy expansion method TaxoExpan, published in WWW 2020

Language: Python - Size: 2.95 MB - Last synced at: 17 days ago - Pushed at: over 3 years ago - Stars: 76 - Forks: 18

sparna-git/skos-play

SKOS-Play allows to print SKOS files in HTML or PDF. It also embeds xls2rdf to generate RDF from Excel.

Language: Java - Size: 40.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 73 - Forks: 14

morningmoni/TaxoRL

Code for paper "End-to-End Reinforcement Learning for Automatic Taxonomy Induction", ACL 2018

Language: Python - Size: 2.94 MB - Last synced at: 17 days ago - Pushed at: over 6 years ago - Stars: 64 - Forks: 13

ArctosDB/arctos

Arctos is a museum collections management system

Size: 68.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 61 - Forks: 13

maxent-ai/zeroshot_topics

Topic Inference with Zeroshot models

Language: Python - Size: 56.6 KB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 61 - Forks: 7

muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Language: C++ - Size: 149 MB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 60 - Forks: 13

oracuk/oisru

Repository for the Open Information Security Risk Universe

Language: Shell - Size: 22.4 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 58 - Forks: 10

bhushankummar/eBay-node-client

Ebay NodeJS Wrapper

Language: JavaScript - Size: 156 KB - Last synced at: 22 days ago - Pushed at: about 1 year ago - Stars: 56 - Forks: 19

daggerhart/taxonomy-term-image

Example plugin for adding an image upload field to taxonomy terms in WordPress

Language: PHP - Size: 40 KB - Last synced at: 9 days ago - Pushed at: over 5 years ago - Stars: 55 - Forks: 19

smdabdoub/kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Language: Python - Size: 43.9 KB - Last synced at: about 7 hours ago - Pushed at: about 3 years ago - Stars: 54 - Forks: 17

shenwei356/gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

Language: R - Size: 329 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 53 - Forks: 3

KennthShang/PhaBOX

Local version of the virus identification and analysis web server (tool set)

Language: Python - Size: 21.2 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 49 - Forks: 5

CatalogueOfLife/general

The Catalogue of Life

Size: 90.5 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 49 - Forks: 5

ropensci/taxa

taxonomic classes for R

Language: R - Size: 20.7 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 47 - Forks: 12

joergmlpts/nature-id

Identify plants, birds, and insects in photos. Should an identification to species be unsuccessful, an identification to a higher taxonomic level - like genus, family, or order - is made.

Language: Python - Size: 1.64 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 44 - Forks: 4

pirovc/multitax

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Language: Python - Size: 295 KB - Last synced at: 16 days ago - Pushed at: 9 months ago - Stars: 44 - Forks: 4

ropensci/taxonomy

taxonomy R packages

Language: HTML - Size: 31.3 KB - Last synced at: 26 days ago - Pushed at: about 1 year ago - Stars: 44 - Forks: 4

JensUweUlrich/Taxor

Fast and space-efficient taxonomic classification of long reads

Language: C++ - Size: 716 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 43 - Forks: 2

yegor256/awesome-risks

Sample Risks for a Software Project

Size: 8.79 KB - Last synced at: 22 days ago - Pushed at: about 1 year ago - Stars: 43 - Forks: 6

ropensci/rotl

Interface to Open Tree of Life API

Language: R - Size: 1.74 MB - Last synced at: 3 days ago - Pushed at: almost 2 years ago - Stars: 42 - Forks: 17

viralemergence/virion

An open database of vertebrate-virus interactions

Language: R - Size: 1.58 GB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 40 - Forks: 8

pyinat/naturtag

Tag your nature photos with iNat taxonomy and observation metadata

Language: Python - Size: 114 MB - Last synced at: about 9 hours ago - Pushed at: 9 days ago - Stars: 40 - Forks: 4

bioforensics/pytaxonkit

Python bindings for the TaxonKit library

Language: Python - Size: 141 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 39 - Forks: 4

DerwenAI/mkrefs

MkDocs plugin to generate semantic reference Markdown pages from a knowledge graph

Language: Python - Size: 298 KB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 37 - Forks: 0

HadrienG/taxadb

:hatching_chick: locally query the ncbi taxonomy

Language: Python - Size: 38.2 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 37 - Forks: 16

jhuapl-bio/taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

Language: Python - Size: 115 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 35 - Forks: 5

LottePronk/whokaryote

Classify metagenomic contigs as eukaryotic or prokaryotic

Language: Python - Size: 8.29 MB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 35 - Forks: 7

telatin/gan

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

Language: Python - Size: 8.82 MB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 35 - Forks: 6

Rundiz/nested-set

The PHP nested set model for create/read/update/delete the tree data structure (hierarchy).

Language: PHP - Size: 941 KB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 34 - Forks: 11

data-solution-automation-engine/TEAM

The Taxonomy for ETL Automation Metadata (TEAM) is a tool for design metadata management geared towards data warehouse automation. It is part of the ecosystem for data warehouse automation, alongside the Virtual Data Warehouse template manager and the generic schema for Data Solution Automation.

Language: C# - Size: 15 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 34 - Forks: 8

insight-centre/saffron

Saffron 4 - Text Analysis and Insight Tool

Language: HTML - Size: 139 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 34 - Forks: 5

sckott/pytaxize

python port of taxize (taxonomy toolbelt) for R

Language: Python - Size: 11.3 MB - Last synced at: 8 days ago - Pushed at: over 4 years ago - Stars: 34 - Forks: 13

milangritta/Pragmatic-Guide-to-Geoparsing-Evaluation

Full resources supporting the publication "A Pragmatic Guide to Geoparsing Evaluation."

Language: Python - Size: 17.6 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 34 - Forks: 4

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

Language: Nextflow - Size: 63.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 33 - Forks: 7

alnv/catalog-manager

Backend Module ohne Programmierkenntnisse erstellen.

Language: PHP - Size: 2.79 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 33 - Forks: 9

about-code/glossarify-md

A Term-to-Definition-Linker for Markdown. https://npmjs.com/package/glossarify-md

Language: JavaScript - Size: 2.28 MB - Last synced at: 30 days ago - Pushed at: over 1 year ago - Stars: 32 - Forks: 8

bio-miga/miga

MiGA: Microbial Genomes Atlas

Language: Ruby - Size: 4.15 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 31 - Forks: 9

ropensci/taxizedb

Tools for Working with Taxonomic SQL Databases

Language: R - Size: 415 KB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 31 - Forks: 8

openooh/venue-taxonomy

The intention of this project is to standardize the list of venue types that represent Digital-Out-of-Home (DOOH) advertising screens within a programmatic OpenRTB 2.5 context. The systematization of DOOH venue types will allow for clearer targeting by media buying platforms across a spectrum of available supply-side platforms offering DOOH inventory.

Size: 342 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 31 - Forks: 31

HiveGuard-AI/taxonomy4good

Taxonomy4Good: a sustainability lexicon that provides the freedom to create custom taxonomies in addition to listed ESG and Sustainability Standards taxonomies.

Language: Python - Size: 3.48 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 31 - Forks: 5

shenwei356/taxid-changelog

NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.

Language: R - Size: 3.89 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 30 - Forks: 1

baskargroup/BioTrove

NeurIPS 2024 Track on Datasets and Benchmarks (Spotlight)

Language: Jupyter Notebook - Size: 195 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 29 - Forks: 4

uhh-lt/taxi

TAXI: a Taxonomy Induction Method based on Lexico-Syntactic Patterns, Substrings and Focused Crawling

Language: Jupyter Notebook - Size: 23.2 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 29 - Forks: 10

uhh-lt/Taxonomy_Refinement_Embeddings

Taxonomy refinement method to improve domain-specific taxonomy systems.

Language: Python - Size: 3.74 MB - Last synced at: 17 days ago - Pushed at: 12 months ago - Stars: 28 - Forks: 2

althonos/pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

Language: Rust - Size: 2.79 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 27 - Forks: 1

obophenotype/ncbitaxon

Build for NCBITaxon

Language: Python - Size: 6.49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 7

ropensci/worrms

World Register of Marine Species R client

Language: R - Size: 369 KB - Last synced at: about 9 hours ago - Pushed at: over 1 year ago - Stars: 27 - Forks: 9

electric-capital/crypto-audits

A mapping for open source cryptocurrency, blockchain, and decentralized audit reports and bug bounties

Size: 45.9 KB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 27 - Forks: 10

rinvex/laravel-tags 📦

Rinvex Taggable is a polymorphic Laravel package, for tag management. You can tag any eloquent model with ease, and utilize the awesomeness of Sluggable, and Translatable models out of the box.

Language: PHP - Size: 319 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 27 - Forks: 8