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The software enable to retrieve information (exon boundaries, mutation effect, known SNP...) about transcribed SNP. It's based on ensembl API.

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process.

TilSeg is a tool designed to use the information from contiguous probes and it will merge them into longer segment stretches. Depending on the experiment, the chip type and the statistical analysis made, those segments may have different meanings and

PAQmiR : Prediction Annotation and Quantification of miRNA with miRDeep2

"clariTE.pl" is a program that post process the xm output file of RepeatMasker.

DRAP is a De novo Rna Assembly Pipeline allowing to clean and filter RNA-seq De novo assemblers results to get the most compact and complete set of transcripts.

Multiple is a program for de novo discovery of DNA motifs corresponding to Transcription Factor binding sites based on a probabilistic model of the DNA sequence that incorporates expression data as covariates.

Some scripts for the methylation analysis of the ChickStress project.

Adaptation of miRDeep2.0.0.5 for dicotyledons, with replaced scripts in which parameters were optimized for dicot plants. This parameters come from Characterization of statistical features for plant microRNA prediction-Thakur V &al -BMC Genomics

Modified of the code CleaveLand to have the results for all isoforms. CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Addo-Quaye C &. Bioinformatics.

Tutorial example for creation of a snakemake workflow using a singularity container on a hpc

Some scripts for the methylation analysis of the ChickStress project.