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AMAPVox, LiDAR data voxelisation software

Copyright (c) https://www.ird.fr (Institut de Recherche pour le Développement) 2016-2022

https://amapvox.org

dojo snakemake assemblage long reads

This pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER which use GeneMark-EX and AUGUSTUS. And the other tool is AUGUSTUS alone for improve annotation of small coding sequences with few or no intron. Before the annotation, the repeat element of genome are masked for avoid annotation probleme. In addition this workflows can perform a illumina assembly with ABySS using différent value of kmere.

Annotation of virulence factor of fungi (Effector , Cazyme ...)

Count, merge, split, rename, and other usefull tools for FASTA sequences files

FOTO for FOurier transform Textural Ordination

Predicting stand structure parameters for tropical forests from remotely sensed data by defining an index of canopy texture from the ordination of the Fourier spectra computed for tropical rain forest images.

A, still very experimental, R package that acts as a storage location for functions and interfaces in connection with genomics (genomes, transcriptomes, annotation, phylogenomics, ...)

GeVarLi pipeline for AFROSCREEN ANRS

Inference of significant kmers under selection

Materials for Learning Bioinformatics and Enhancing Competencies - Git

Application of the FAO-56 formalism with used of remote-sensing daily NDVI forcing to estimate evapotranspiration and irrigation amounts at field scale . Main formalism is from SAMIR tool (CESBIO Lab).