samm82/TestingTesting

My MASc thesis: Putting Software Testing Terminology to the Test

Language: TeX - Size: 381 MB - Last synced at: about 6 hours ago - Pushed at: about 7 hours ago - Stars: 0 - Forks: 0

soedinglab/MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

Language: C - Size: 30.6 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1,650 - Forks: 222

rseng/software

research software encyclopedia database

Language: Shell - Size: 39.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 14 - Forks: 6

AaltoDictionaryofML/AaltoDictionaryofML.github.io

Welcome! 👋 This is the working draft of the Aalto Dictionary of Machine Learning (ADictML) — a growing collection of short, clear definitions for key terms in machine learning.

Language: TeX - Size: 44.1 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 7

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: 4 days ago - Pushed at: 4 days ago - Stars: 34 - Forks: 11

SpeciesFileGroup/taxonworks

Workbench for biodiversity informatics.

Language: Ruby - Size: 97.5 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 96 - Forks: 30

steineggerlab/Metabuli

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

Language: C++ - Size: 17.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 138 - Forks: 12

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: 4 days ago - Pushed at: 4 days ago - Stars: 27 - Forks: 1

antonheitz/xBRL-Forge

Open Source iXBRL Report, xBRL Report and xBRL Taxonomy Generator

Language: Python - Size: 1.36 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 2

sonata-project/SonataClassificationBundle

Symfony SonataClassificationBundle

Language: PHP - Size: 1.6 MB - Last synced at: 2 days ago - Pushed at: 4 days ago - Stars: 91 - Forks: 112

oldvis/image-taxonomy

📖A taxonomy of old visualizations

Size: 368 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 0

oldvis/image-taxonomy-labeler

🖥️A labeling interface for image taxonomy labeling and comparison

Language: Vue - Size: 96.9 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

ICTV-Virus-Knowledgebase/ICTVdatabase

ICTV taxonomy database - data export, schema and maintenance scripts

Language: TSQL - Size: 76.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

JensUweUlrich/Taxor

Fast and space-efficient taxonomic classification of long reads

Language: C++ - Size: 716 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 43 - Forks: 2

KennthShang/PhaBOX

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

Language: Python - Size: 21.2 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 49 - Forks: 5

MISP/misp-taxonomies

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

Language: Python - Size: 3.67 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 274 - Forks: 139

moshi4/ANIclustermap

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

Language: Python - Size: 184 MB - Last synced at: 6 days ago - Pushed at: 10 days ago - Stars: 79 - Forks: 9

wp-cli/entity-command

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

Language: PHP - Size: 8.74 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 101 - Forks: 93

electric-capital/crypto-ecosystems

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

Language: Zig - Size: 176 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,733 - Forks: 1,575

bioforensics/pytaxonkit

Python bindings for the TaxonKit library

Language: Python - Size: 141 KB - Last synced at: about 2 hours ago - Pushed at: about 3 hours ago - Stars: 39 - Forks: 4

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: 6 days ago - Pushed at: 7 days ago - Stars: 412 - Forks: 32

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: 7 days ago - Pushed at: 7 days ago - Stars: 30 - Forks: 1

openfoodfacts/taxonomy-editor

Taxonomies are at the heart of Open Food Facts data structure - this project provides an editor

Language: Python - Size: 3.38 MB - Last synced at: 1 day ago - Pushed at: 7 days ago - Stars: 19 - Forks: 25

faubulous/mentor-vscode

Visual Studio Code extension providing editing support for RDF languages and knowledge graphs.

Language: TypeScript - Size: 5.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 18 - Forks: 0

angelosalatino/kos-rf

A Survey on Knowledge Organization Systems of Research Fields: Resources and Challenges

Language: HTML - Size: 79.3 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 9 - Forks: 0

pyinat/naturtag

Tag your nature photos with iNat taxonomy and observation metadata

Language: Python - Size: 114 MB - Last synced at: 3 days ago - Pushed at: 10 days ago - Stars: 40 - Forks: 4

viralemergence/virion

An open database of vertebrate-virus interactions

Language: R - Size: 1.06 GB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 39 - Forks: 8

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: 5 days ago - Pushed at: 5 days ago - Stars: 34 - Forks: 5

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: 1 day ago - Pushed at: 3 months ago - Stars: 202 - Forks: 19

alnv/catalog-manager

Backend Module ohne Programmierkenntnisse erstellen.

Language: PHP - Size: 2.78 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 33 - Forks: 9

SpeciesFileGroup/taxonpages

TaxonPages is a tool to serve TaxonPages.

Language: CSS - Size: 1.27 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 10 - Forks: 37

nfdi4cat/voc4cat

A SKOS vocabulary for catalysis maintained by NFDI4Cat & friends

Language: Just - Size: 5.56 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 11 - Forks: 11

lepitaxa/lepitaxa.github.io

LEPITAXA – Lepidopteran Classification Project

Language: HTML - Size: 2.25 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 0

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

Language: R - Size: 468 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 495 - Forks: 148

CatalogueOfLife/checklistbank

UI for checklistbank.org

Language: JavaScript - Size: 10.5 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 7 - Forks: 3

Changwanseo/FunVIP

Fungal Validation and Identification Pipeline

Language: Python - Size: 119 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 10 - Forks: 0

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: 14 days ago - Pushed at: 14 days ago - Stars: 517 - Forks: 84

shenwei356/gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

Language: R - Size: 329 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 53 - Forks: 3

collective/collective.taxonomy

Create, edit and use hierarchical taxonomies in Plone!

Language: Python - Size: 70 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 18 - Forks: 24

bio-org-au/services-g3

Grails 3 port of NSL services

Language: Groovy - Size: 6 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

paintparty/lasertag

Lasertag is a library for categorizing types of values in Clojure, ClojureScript, and Babashka

Language: Clojure - Size: 289 KB - Last synced at: 7 days ago - Pushed at: 17 days ago - Stars: 4 - Forks: 0

ropensci/taxize

A taxonomic toolbelt for R

Language: R - Size: 36.6 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 277 - Forks: 62

khustochka/kjogvi

Language: Elixir - Size: 1.98 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

andybywire/sanity-plugin-taxonomy-manager

Create and manage SKOS compliant taxonomies, thesauri, and classification schemes in Sanity Studio.

Language: TypeScript - Size: 50.8 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 23 - Forks: 6

ropensci/rotl

Interface to Open Tree of Life API

Language: R - Size: 1.74 MB - Last synced at: 5 days ago - Pushed at: almost 2 years ago - Stars: 42 - Forks: 17

tientq64/taxon4

🐚 Collect and classify species of organisms.

Language: TypeScript - Size: 5.8 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 8 - Forks: 0

seoul-wordpress-meetup/swpmu-term-merger

워드프레스를 위한 심플한 텀 병합 플러그인

Language: TypeScript - Size: 1.9 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 1

xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

Language: Nextflow - Size: 3.62 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 2 - Forks: 1

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.8 MB - Last synced at: 10 days ago - Pushed at: 2 months ago - Stars: 146 - Forks: 27

alrichardbollans/wcvpy

Packages for downloading the World Checklist of Vascular Plants (WCVP) and resolving plant names to it

Language: Python - Size: 6.18 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 2 - Forks: 0

althonos/pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

Language: Cython - Size: 421 KB - Last synced at: 21 days ago - Pushed at: 27 days ago - Stars: 22 - Forks: 1

ecoinfor/U.Taxonstand

R package for standardizing and harmonizing scientific names of plants and animals

Language: R - Size: 2.95 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 21 - Forks: 0

luomus/finbif

R interface for the Finnish Biodiversity Information Facility (FinBIF) API

Language: R - Size: 70.7 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 5 - Forks: 1

codeboxrcodehub/cbxtaxonomy

WordPress helper plugin for creating custom taxonomy (category, tag) inside WordPress

Language: PHP - Size: 1.72 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

bugcrowd/vulnerability-rating-taxonomy

Bugcrowd’s baseline priority ratings for common security vulnerabilities

Language: Python - Size: 518 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 474 - Forks: 92

ropensci/rfishbase

R interface to the fishbase.org database

Language: R - Size: 265 MB - Last synced at: 3 days ago - Pushed at: 4 months ago - Stars: 117 - Forks: 42

tetsufmbio/taxallnomy

Taxallnomy is a balanced taxonomic tree database based on NCBI Taxonomy that provides taxonomic lineages according to the taxonomic ranks of Linnean classification system.

Language: Perl - Size: 216 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 13 - Forks: 2

baskargroup/BioTrove

NeurIPS 2024 Track on Datasets and Benchmarks (Spotlight)

Language: Jupyter Notebook - Size: 195 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 29 - Forks: 4

8Ginette8/gbif.range

An R package to generate species range maps based on ecoregions and a user-friendly GBIF wrapper

Language: R - Size: 220 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 16 - Forks: 1

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: 13 days ago - Pushed at: about 3 years ago - Stars: 54 - Forks: 17

unipept/unipept-visualizations

📊 Unipept visualisations, packaged for easy reusability

Language: TypeScript - Size: 47.6 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 18 - Forks: 6

esteinig/scrubby

Host depletion optimised for clinical metagenomic sequencing applications :panda_face:

Language: Rust - Size: 581 KB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 16 - Forks: 2

CycloneDX/cyclonedx-property-taxonomy

A taxonomy of all official CycloneDX property namespaces and names

Language: Ruby - Size: 170 KB - Last synced at: 5 days ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 34

zyxue/ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

Language: Python - Size: 395 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 144 - Forks: 30

PoisotLab/NCBITaxonomy.jl

Wrapper around the NCBI taxonomy files

Language: Julia - Size: 2.83 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 2

justin-tpb/TaxIDs-to-SankeyMATIC

Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.

Language: Python - Size: 109 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

marz1877/Language_Code_Advanced

Language standard code that illustrates hierarchies and similarities.

Size: 32.2 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sitegeist/Sitegeist.Taxonomy

Manage vocabularies and taxonomies as separate node-hierarchy.

Language: JavaScript - Size: 1.41 MB - Last synced at: 22 days ago - Pushed at: about 1 month ago - Stars: 14 - Forks: 15

unipept/umgap

A taxonomic classifier for shotgun metagenomics reads

Language: Rust - Size: 27.7 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 6

poeli/detaxa

A flexible, adaptable, and well-defined python package for taxonomy and accession number lookup.

Language: Python - Size: 313 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

blekhmanlab/MicroBioMap

R package for fetching and parsing data of the Human Microbiome Compendium

Language: R - Size: 6.78 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 10 - Forks: 4

muellan/metacache

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

Language: C++ - Size: 149 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 59 - Forks: 13

peterbat1/processALA

R package to give easy access to ALA plant occurrence data

Language: R - Size: 39.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1

guigolab/biogenome-portal

Biogenome data portal

Language: Vue - Size: 148 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 2

builtenvdata/experiments-website

Explore datasets with ease using taxonomy filtering, allowing you to quickly identify the specific experimental datasets you need and download them effortlessly

Size: 8.14 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

ebi-jdispatcher/taxonomy-resolver

Builds lists of Taxonomy Identifiers based on the NCBI Taxonomy Database

Language: Python - Size: 109 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 3

pr2database/pr2database

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

Language: R - Size: 761 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 80 - Forks: 7

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 1 month ago - Pushed at: about 1 month ago - Stars: 96 - Forks: 12

yzhan238/TELEClass

The source code used for paper "TELEClass: Taxonomy Enrichment and LLM-Enhanced Hierarchical Text Classification with Minimal Supervision", published in WWW 2025.

Language: Python - Size: 144 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

deckerweb/post-author-taxonomy

Simple & lightweight: Registers a simple post authors taxonomy for the regular Posts post type. The taxonomy is not hierarchical, so it's similar to tags but for authors instead. Shortcodes for a list of authors and an Author Box are included.

Language: PHP - Size: 23.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

phyloverse/phyloverse.github.io

Ph.D. candidate in Botany, University of Wisconsin-Madison

Language: CSS - Size: 24.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

CERT-LT/MISP-taxonomy

Kibernetinių incidentų taksonomija

Size: 10.7 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

shanedrabing/taxopedia

Taxonomic trees (cladograms) from Wikipedia-scraped data.

Language: Python - Size: 1.66 MB - Last synced at: 21 days ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 1

lverweijen/littletree

Tree backed by dictionary

Language: Python - Size: 319 KB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

bioinformatics-centre/kaiju

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

Language: C - Size: 906 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 278 - Forks: 67

CVUA-RRW/taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files

Language: Python - Size: 1.01 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 1 - Forks: 2

tznurmin/TEA

Taxonomic Entity Augmentation makes biomedical texts less repetitive

Language: Python - Size: 161 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

ropensci/taxa

taxonomic classes for R

Language: R - Size: 20.7 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 47 - Forks: 12

wikibonsai/wikibonsai

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

Language: Svelte - Size: 37.8 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 77 - Forks: 3

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

Language: Nextflow - Size: 60.3 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 33 - Forks: 7

Lecturize/Laravel-Taxonomies

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

Language: PHP - Size: 155 KB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 99 - Forks: 29

CallinCeriani/blast2tree

Extract and compare single copy DNA sequences of taxonomic interest

Language: Shell - Size: 269 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

NishDJ/UNIVERSAL_CATEGORIES

Language: JavaScript - Size: 213 KB - Last synced at: 30 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

steineggerlab/taxoview

A Vue.js plugin for generating interactive Sankey diagrams using Kraken report data

Language: Vue - Size: 229 KB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 5 - Forks: 1

gbif/hp-solanaceae

Solanaceae Source - a global resource for the taxonomy of the nightshade family

Language: HTML - Size: 358 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

huiqingyeooo/aedini_review

A collection of scripts and useful information for generating figures for a review paper on aedini phylogenies

Language: R - Size: 4.88 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

ali5ter/cli_taxo

Experiments in displaying CLI command taxonomy

Language: HTML - Size: 1.44 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 2

ouzounis/kurimu Fork of bcpl-certh/kurimu

Kurīmu (meaning “cream” in Japanese) is a pangenome data collection for public access.

Language: HTML - Size: 156 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

obophenotype/ncbitaxon

Build for NCBITaxon

Language: Python - Size: 6.49 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 27 - Forks: 7

bio-miga/miga

MiGA: Microbial Genomes Atlas

Language: Ruby - Size: 4.14 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 31 - Forks: 9