Learning from Crowds with Crowd-Kit
Learning from Crowds with Crowd-Kit - Published in JOSS (2024)
Crowsetta
Crowsetta: A Python tool to work with any format for annotating animal vocalizations and bioacoustics data. - Published in JOSS (2023)
corpus-annotation-graph-builder
Corpus Annotation Graph builder (CAG) is an architectural framework that employs the build-and-annotate pattern for creating a graph.
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://github.com/brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
metagenome-atlas
ATLAS - Three commands to start analyzing your metagenome data
cvat
Annotate better with CVAT, the industry-leading data engine for machine learning. Used and trusted by teams at any scale, for data of any scale.
fafbseg
Tools to work with the FlyWire connectome. Fully interoperable with navis.
recognizer
A tool for domain based annotation with databases from the Conserved Domains Database
obofoundry.github.io
Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
lidia-zotero
Zotero plugin for capturing PDF reader annotations for the LIDIA project
MetaboAnnotation
High level functionality to support and simplify metabolomics data annotation.
genomeannotator
Pipeline for the identification of (coding) gene structures in draft genomes.
https://github.com/centrefordigitalhumanities/textminer
A script to detect named entities and store them in an Elasticsearch annotated_text field
https://github.com/doccano/doccano-transformer
The official tool for transforming doccano format into common dataset formats.
annotatr
Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
https://github.com/compnet/wikisynch
Synchronization between two Wikipedia-based Corpora
https://github.com/cdli-gh/annodoc
Annotation documentation for Sumerian annotation within CDLI/MTAAC
documentarist
Process Caltech Archives' digital documents and photos, and annotate each page or image with information about its contents
vision6d
6D Pose Annotation Tool and Real-time Visualization - Vision6D for supporting users to annotate the 6D pose of a given 3D object for any given 2D images and depth estimation. This 6D pose annotation tool supports annotate videos and a set of 2D images.
https://github.com/hcmlab/nova
NOVA is a tool for annotating and analyzing behaviours in social interactions. It supports Annotators using Machine Learning already during the coding process. Further it features both, discrete labels and continuous scores and a visuzalization of streams recorded with the SSI Framework.
https://github.com/ai4bharat/shoonya
Shoonya - Platform to Annotate and label data at scale.
deep_active_learning_biore
Framework to study the use of deep active learning for biomedical relation extraction
digitaldramaturgy.github.io
Play script annotation and dramaturgical interpretation platform. Built On CollectionBuilder CSV.
annodash
[JAMIA Open] A clinical terminology annotation dashboard created using Plotly Dash & the MIMIC-IV database.
bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
kabr-tools
Tools for working with data for annotating animal behavior. These were specifically designed during construction of the KABR dataset.
toxic-video-games-gnn
Toxic video game classification with graph neural networks
nf-platypusindelcalling
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
https://github.com/alexisvassquez/juniper2.0
Conversational AI model and educational tool
smallvariants
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
Jabberwocky
Jabberwocky: an ontology-aware toolkit for manipulating text - Published in JOSS (2020)
2018-neon-beetles-processing
Processing code and exploratory notebooks for BeetlePalooza dataset (2018 NEON Ethanol-preserved Ground Beetles).
wacline
WacLine is a software product line that allows configuration and derivation of web annotation browser extensions for specific domains using pure::variants
msannika_csm_annotation
Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.
Syclops
Syclops: A Modular Pipeline for Procedural Generation of Synthetic Data - Published in JOSS (2025)