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 simple python library to identify the most likely strain from the population

SPIRO is a Smart Plate Imaging Robot

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

HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).

Genomic prediction of amino acid traits in Arabidopsis seeds

Nextflow pipeline to assemble genomes from long reads.

A pipeline to analyse small RNA expression using Illumina sequencing data

🌱🧬 Collection of scripts for the paper: "PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave" (The Plant Cell 2022; PMID 35404429 🔗)

An automated pipeline for analyzing arabidopsis luciferase imaging data

Python scripts related to the At7 sequencing project

Arabidopsis EcoGEx (R-📦 + 🕸️-App)

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

Regularly updated version of `org.At.tair.db`.

phylogenomics analysis for arabidopsis maf-cap genes

Interactive Functional Annotations Dashboard

Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)

Clustering of 1,135 Arabidopsis thaliana genomes from 1001 Genomes Project (https://1001genomes.org/)

🌱🧬 Collection of scripts for the paper: 📑 "Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways" (The Plant Cell 2020; PMID 32213639 🔗)

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