A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

A data visualization tool to display tissue expression data for Arabidopsis thaliana

A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.

A web based app developed using the R package shiny to explore the transcriptional network downstream from the Arabidopsis thaliana transcriptional factor BRC1.

Arabidopsis Thaliana TRanscriptionAl Circadian neTwORk, a web based tool developed using the R package shiny for the exploration and analysis of a transcriptional network in Arabidopsis thaliana constituted by circadian and light responsive transcriptional factors and regulators

The related code of the master thesis, "Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thaliana"

Nextflow pipeline to assemble genomes from long reads.

A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species

Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA

Division event and resulting topological changes prediction of Arabidopsis thaliana shoot apical and floral meristems

Scripts associated with understanding the genomic features of NLRs in Arabidopsis thaliana Col-0

The repository contains all the scripts necessary for the bioinformatic characterisation of the IDRs of Arabidopsis transcription factors.

Simulation of hydraulic root architecture

On étudie dans ce projet les éléments transposables de l’Arabidopsis thaliana. L’objectif de ce projet est de concevoir une base de données regroupant l’ensemble des copies, ainsi que les copies de référence, de six familles d’éléments transposables issues du génome TAIR10 de l’Arabidopsis thaliana, sélectionnées par nos soins.

Bioinformatics pipeline for lncRNA prediction in Arabiodpsis thaliana

A website to explore biological relationships between Arabidopsis thailiana genetic characteristics.

🌱 Reconstruct genetic regulation timelines in _Arabidopsis thaliana_ using causal inference, addressing missing data and parameter selection challenges effectively.

Gene ID Retrieval from TAIR: R code to retrieve gene IDs from TAIR (The Arabidopsis Information Resource) and export them as CSV files

💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across model organisms using Gene Ontology annotation extension. 🎓 Part of my PhD project, King's College London (2013-2019).