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Pipeline Nextflow

Some scripts for the methylation analysis of the ChickStress project.

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

A new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S, 23S rRNA genes amplicons DOI: 10.5281/zenodo.3678129

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.

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

Family-Companion: analyse, visualise, browse, query and share your homology clusters Ludovic Cottret, Corinne Rancurel, Martial Briand, Sebastien Carrere BioArxiv, doi: https://doi.org/10.1101/266742

Some scripts for the methylation analysis of the ChickStress project.

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

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.

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

PAQmiR : Prediction Annotation and Quantification of miRNA with miRDeep2