Search Results for "annotation"
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Showing 27 open source projects for "annotation"
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Diffgram
Training data (data labeling, annotation, workflow) for all data types
...This is aimed to reduce your data labeling bills and increase your Training Data Quality. Training Data is the art of supervising machines through data. This includes the activities of annotation, which produces structured data; ready to be consumed by a machine learning model. Annotation is required because raw media is considered to be unstructured and not usable without it. That’s why training data is required for many modern machine learning use cases including computer vision, natural language processing and speech recognition. -
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ggforce
Accelerating ggplot2
ggforce is an extension package for ggplot2 that introduces specialized statistical transforms, geoms, and layout utilities to enhance and complement the built-in ggplot2 offerings. It enables more advanced visualization techniques such as faceting enhancements, hulls, annotation marks, and novel layouts for network data and marked regions. -
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Datumaro
Dataset Management Framework, a Python library and a CLI tool to build
...It supports importing and exporting annotations and images across a wide variety of standards like COCO, PASCAL VOC, YOLO, ImageNet, Cityscapes, and many more, enabling easy integration with different training pipelines and tools. Datumaro makes it easy to merge datasets, split them into training/validation/test subsets, filter or transform annotations, and validate annotation quality — all while preserving metadata and supporting detailed statistics. It’s especially useful when you’re dealing with heterogeneous data sources or need to prepare complex datasets for machine learning workflows, freeing you from writing custom scripts for every format conversion. -
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FiftyOne
The open-source tool for building high-quality datasets
...Use it to get hands-on with your data, including visualizing complex labels, evaluating your models, exploring scenarios of interest, identifying failure modes, finding annotation mistakes, and much more! Surveys show that machine learning engineers spend over half of their time wrangling data, but it doesn't have to be that way. -
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ggpubr
'ggplot2' Based Publication Ready Plots
ggpubr is an R package that provides easy-to-use wrapper functions around ggplot2 to create publication-ready visualizations with minimal code. It streamlines plot creation for researchers and analysts, allowing features such as statistical annotation, theme customization, and plot arrangement with fewer lines of code. -
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clusterProfiler
A universal enrichment tool for interpreting omics data
clusterProfiler is an R/Bioconductor package that provides a unified workflow for functional enrichment analysis to interpret high-throughput omics results. It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can... -
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Superstruct
A simple and composable way to validate data in JavaScript
This project is a lightweight validation library for JavaScript and TypeScript that helps you define data “shapes” and validate runtime values against them. Instead of relying only on compile-time typing, it focuses on the reality that many apps receive unknown input from APIs, forms, and external systems, and those values need runtime checks. Its API is intentionally familiar if you’ve used TypeScript, Flow, Go structs, or GraphQL schemas, but the output is oriented around runtime... -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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Strings Edit
String editing and formatting library for Ada
Strings edit is a library that provides I/O facilities for integers, floating-point numbers, Roman numerals, and strings. Both input and output subroutines support string pointers for consequent stream processing. The output can be aligned in a fixed size field with padding. Numeric input can be checked against expected values range to be either saturated or to raise an exception. For floating-point output either relative or absolute output precision can be specified. UTF-8 encoded strings... -
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VectreViewer: A vector-based file viewer
A Windows-based viewer currently supporting CDR & 2D DXF files
This is a Windows-based wireframe viewer currently designed for CDR & 2D R12 DXF files. The DXF renderer supports arcs, circles, lines and polylines. Support for SVG files is coming shortly. Go here to check for updates: https://www.vvwr.net -
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DataGym.ai
Open source annotation and labeling tool for image and video assets
...Your image data can be imported into DATAGYM from your local machine, from any public image URL or directly from an AWS cloud S3 bucket. Machine learning teams spend up to 80% of their time on data preparation. DATAGYM provides AI-powered annotation functions to help you accelerate your labeling task. The Pre-Labeling feature enables turbo-labeling – it processes thousands of images in the background within a very short time. -
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scArches
Reference mapping for single-cell genomics
Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations. -
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GAPE
proteogenomic analysis software
GAPE is a one-stop proteogenomic informatics software that provides a multifaceted and standard workflow against eukaryotes in proteogenomic data-analysis cycle for genome refinement and global identification of PTM events. This software allows concurrent querying of proteomic and genomic databases to refining the genome and proteome annotations comprehensively. This includes MS data and database construction, database searches, FDR calculations, statistical result integration, validation of... -
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ParTools
Support for manual parallelization of sequential C programs.
ParTools allows the interactive analysis of a C program execution profile and data dependencies to facilitate the discovery and selection of suitable parallelization candidates in a manual parallelization process. The flow does not assume any specific parallelization technique, thus it can be broadly applied. The original (serial) C source is automatically annotated to trace the execution profile and data dependencies at run-time. The annotated program is then executed using a... -
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AlertWheel
AlertWheel is a visualization-based analysis tool for Snort IDS logs
...AlertWheel simultaneously combines three link bundling techniques in a novel way to reduce cluttering on the interface. Our solution also incorporates filtering options, annotation, logging and details-on-demand, to support analysis processes as described by specialists in this field. This project was developed as a prototype for a research paper. Not designed for production use. No support will be offered for production installations. See documentation for prerequisites. -
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pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..
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Ondex Web
Web-based visualisation of networks using Java
Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL -
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Research and development of an ontology for the analysis and representation of comparative data for use in evolutionary analysis. For more information, please see www.evolutionaryontology.org
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DMETANALYZER
A tool for supporting pharmacogenomics data analysis
We developed DMET-Analyzer a tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way. -
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Xi Spectrum Viewer
Mass Spectrum Viewer Tool
To overcome current limitations in published MS data accessibility, we introduce a browser-based spectrum viewer that aims to allow exploration of alternative interpretations for MS spectra and additionally: can be operated by non-specialists, is open source, can be integrated into other software, gives appropriate publication-quality output. Spectrum Viewer is implemented totally on the client side using XHTML for menus and dialogs, SVG for spectrum and peptide display, and Javascript to... -
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The Functional Genomics Data Society develops standards for biological research data quality, annotation and exchange. We define minimum information specs and create software that builds on these, helping scientists annotate and share data easily.
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Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.
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Replaytool provides an environment for the replay and annotation of multiple media sources, such as video files, text logs, map data etc. See www.cs.nott.ac.uk/~apf for some more screenshots and videos.
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Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
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...It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.
