ISA tools (@ISA-tools)

Top repositories

1

isa-api

ISA tools API
Jupyter Notebook
40
star
2

OntoMaton

OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.
JavaScript
40
star
3

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).
Java
40
star
4

stato

This is the development repository for the STATistics Ontology (STATO). For more information and demonstration on the ontology content, please visit its website:
Java
31
star
5

SequenceLogoVis

A better sequence logo visualization
JavaScript
22
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6

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).
R
20
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7

biopy-isatab

Python parser for ISAtab, a biological file format for experimental metadata
Python
16
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8

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).
Java
16
star
9

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).
Java
13
star
10

ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools
Java
12
star
11

mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
Python
12
star
12

linkedISA

Package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies).
Java
12
star
13

ISAdatasets

Repository for ISA datasets, which may be available in different formats (tab, RDF, JSON)
7
star
14

isa-explorer

A lightweight web-based ISA-Tab viewer for multiple ISA-Tab files.
JavaScript
7
star
15

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
Java
7
star
16

mzml2isa-galaxy

mzml2isa for galaxy
6
star
17

graph2tab

graph2tab, a library to convert experimental workflow graphs into tabular formats
Java
6
star
18

jUtils

jUtils, a miscellanea of small and handy general purpose utilities for Java
Java
6
star
19

isatools-notebooks

Example Jupyter notebooks using the ISA-API
Jupyter Notebook
5
star
20

isa-specs

ISA Model and Serialization Specifications
HTML
5
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21

MSIO

Metabolomics Standards Initiative Ontology
Java
5
star
22

frictionless-collab

Frictionless JSON Data Packages for Life Science
Python
5
star
23

FAIRsharing-Owl2Neo

OWL Importer to Neo4j for FAIRsharing
Java
5
star
24

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
5
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25

soapdenovo2

SOAPdenovo2 case study website
Shell
4
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26

Docbooks

Documentation
3
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27

ISAcreatorPlugins

Plugins developed for use in the ISAcreator. They should be placed in a 'Plugins' directory in the ISAcreator build environment.
Java
3
star
28

ISATab-Viewer

An ISA-Tab web viewing library written in Javascript.
JavaScript
3
star
29

NanoMaton

Java
3
star
30

ISAtabErrorReporter

A GUI to display ISAtab errors, showing images of files and listing the errors clearly.
Java
2
star
31

isa-rest-service

RESTful web service to use ISA API
Python
2
star
32

isatools-galaxy

ISA Galaxy tools, tours, and other enhancements
JavaScript
2
star
33

BioSharingUtils

A selection of tools to automatically update content in BioSharing.
Java
1
star
34

BioFormats

BioFormat code developed at WebValley
Java
1
star
35

isa-rwval

Read/write/validation packages for the ISA tools API
Python
1
star
36

linkedISA-ws

RESTful web service for converting ISATab files into RDF, relying on the linkedISA converter..
Java
1
star
37

ISAValidatorWS

Restful Webservice for Validation of ISATab files.
JavaScript
1
star
38

nmrml2isa-galaxy

nmrml2isa for galaxy
HTML
1
star
39

isa-cookbook

ISA python API documentation
JavaScript
1
star
40

MAGEToISAConverterWS

RESTful web service implementation for the MAGEtoISAconverter. You should
Java
1
star
41

SIR-metabolomics-CV

Stable Isotope Resolved Metabolomics Terminology
Web Ontology Language
1
star
42

NovartisMetastore

Connection code to the Novartis metastore
Java
1
star
43

Automacron

Motif finding algorithm and tool to find functionally relevant motifs in workflows.
Java
1
star
44

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.
Java
1
star