ISA-tools/biopy-isatab

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Python
License
MIT License
Created over 13 years ago
Updated almost 8 years ago

ISA-tools/biopy-isatab

ISA-tools

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Python parser for ISAtab, a biological file format for experimental metadata

isa-api

Jupyter Notebook

OntoMaton

OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.

ISAcreator

ISAcreator is a Java desktop application which allows for the creation and editing of ISA-Tab files. Originally developed by Eamonn Maguire, with further contributions by Alejandra Gonzalez-Beltran, David Johnson and Philippe Rocca-Serra (Uni. of Oxford).

stato

This is the development repository for the STATistics Ontology (STATO). For more information and demonstration on the ontology content, please visit its website:

SequenceLogoVis

A better sequence logo visualization

Risa

Risa allows to access metadata/data in ISA-tab format and builds Bioconductor data structures. Apart from parsing ISA-tab files, the package also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).

BioInvIndex

The web application, model, database persistence, services package and web services for the BII. Led by Eamonn Maguire (Uni. of Oxford) & Philippe Rocca-Serra (Uni. of Oxford).

ISAconfigurator

The ISAconfigurator allows for creation of XML files (configuration files) used to build spreadsheets in the ISAcreator and for validation in the creator and ISAvalidation code. Led by Eamonn Maguire, Philippe Rocca-Serra (Uni. of Oxford).

ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools

mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure

linkedISA

Package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies).

ISAdatasets

Repository for ISA datasets, which may be available in different formats (tab, RDF, JSON)

isa-explorer

A lightweight web-based ISA-Tab viewer for multiple ISA-Tab files.

MAGEtoISAconverter

Converter which can pull from ArrayExpress (by an accession number) or read local files and convert them to ISAtab. Lead by Philippe Rocca-Serra & Eamonn Maguire, University of Oxford

mzml2isa-galaxy

mzml2isa for galaxy

graph2tab

graph2tab, a library to convert experimental workflow graphs into tabular formats

jUtils

jUtils, a miscellanea of small and handy general purpose utilities for Java

isatools-notebooks

Example Jupyter notebooks using the ISA-API

Jupyter Notebook

isa-specs

ISA Model and Serialization Specifications

MSIO

Metabolomics Standards Initiative Ontology

frictionless-collab

Frictionless JSON Data Packages for Life Science

FAIRsharing-Owl2Neo

OWL Importer to Neo4j for FAIRsharing

isa-configurations

ISAconfiguration files which have been created by the ISAconfigurator. These can be used by ISAcreator, ISAvalidator, ISAconverter and the BII Data Management Tool

soapdenovo2

SOAPdenovo2 case study website

Docbooks

ISAcreatorPlugins

Plugins developed for use in the ISAcreator. They should be placed in a 'Plugins' directory in the ISAcreator build environment.

ISATab-Viewer

An ISA-Tab web viewing library written in Javascript.

NanoMaton

ISAtabErrorReporter

A GUI to display ISAtab errors, showing images of files and listing the errors clearly.

isa-rest-service

RESTful web service to use ISA API

isatools-galaxy

ISA Galaxy tools, tours, and other enhancements

BioSharingUtils

A selection of tools to automatically update content in BioSharing.

BioFormats

BioFormat code developed at WebValley

isa-rwval

Read/write/validation packages for the ISA tools API

linkedISA-ws

RESTful web service for converting ISATab files into RDF, relying on the linkedISA converter..

ISAValidatorWS

Restful Webservice for Validation of ISATab files.

nmrml2isa-galaxy

nmrml2isa for galaxy

isa-cookbook

ISA python API documentation

MAGEToISAConverterWS

RESTful web service implementation for the MAGEtoISAconverter. You should

SIR-metabolomics-CV

Stable Isotope Resolved Metabolomics Terminology

Web Ontology Language

NovartisMetastore

Connection code to the Novartis metastore

Automacron

Motif finding algorithm and tool to find functionally relevant motifs in workflows.

HelpWebUtility

The web browser in this package has pretty basic functionalities, but is also quite flexible, and for in-app browsing, like that done in IntelliJ for instance, in order to navigate to help pages, it is perfect. I don't need any special JNI calls to invoke browsers therefore I don't introduce platform-dependent code into the codebase.