Tools

The tools below have been developped by i-Trop members or sometimes as part of collaborative projects, especially with other members of the Southgreen platform.

All
itrop
bioanalysis
plants
health
southgreen
datamanagement
database
genome hub
workflow
shiny
bank
visualization

ARIM

ARIM is web_based tool to arthropodes hematophages and soil nematodes collections management.

Coffee Genome Hub

The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee. Data available are the complete genome sequence of C. canephora along with gene structure, gene product information,gene families, transcriptomics, genetic markers and genetic maps.

CMap

CMap is a web-based tool that allows users to view comparisons of genetic and physical maps.

CulebrONT

CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality. CulebrONT can help to choose the best assembly between all possibilities.

DiffExDB

DiffExDB is a web-based tool for exploring gene expression (microarray or RNA-Seq experiments) and differential expression analyses.

EvoLaps

EvoLaps is a user-friendly web application designed to visualize the spatial and temporal spread of pathogens. It takes an annotated tree as entry, such as a maximum clade credibility tree obtained through continuous phylogeographic inference.

Galaxy i-Trop

Galaxy is a web-based scientific analysis platform used to analyze large genomics datasets : making analyses accessible to all researchers, ensuring analyses are completely reproducible (i-Trop resource)

Gigwa

The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype pattern.

INsPECT

INsPECT (INtracellular ParasitE CounTer) is a free and open source software dedicated to automate quantification of Leishmania intracellular parasites based on fluorescent DNA images.

MoccaDB

MoccaDB is a comprehensive web resource for researchers working on Coffea genus, the Rubiaceae family or related species.

P-trap

P-TRAP software (for Panicle TRAits Phenotyping), is a free and open source application for high-throughput measurements of panicle architecture and seed-related traits.

Redcap

REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment (including compliance with 21 CFR Part 11, FISMA, HIPAA, and GDPR), it is specifically geared to support online and offline data capture for research studies and operations. The REDCap Consortium, a vast support network of collaborators, is composed of thousands of active institutional partners in over one hundred countries who utilize and support their own individual REDCap systems.

RegaDB

RegaDB is a HIV database and analysis management environnement. It is used to HIV analysis tool. It is developped by K.U. Leuven.

Rice Genome Hub

The Rice Genome Hub is a an integrative genome information system that allows centralized access to genomics and genetics data .

SNiPlay

SNiPlay is a web-based tool for SNP and polymorphism analysis.

Symptoms Intensity Analysis Tool

Application web to visualize and analyze the mesure of symptom intensity as quantitative variable in function of experimental factors.

TOOGLe

TOGGLe is a workflow manager designed to be as effortless as possible to use for biologists, so the focus can remain on the analyses. Pipelines are easily customizable and analyses are reproducible and shareable. TOGGLe has been tested and used in large-scale projects on various organisms.

Voozanoo

VooIRD is a web-based toolkit used to medical questionnaire to HIV, Ebola and Covid-19. This tool is based on Voozanno developped by Epiconcept

Xanthomonas utilities website

The Xanthomonas utilities website offers a collection of bioinformatic tools developed for the analysis of Xanthomonas genomes.