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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
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A new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S, 23S rRNA genes amplicons DOI: 10.5281/zenodo.3678129
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Tutorial example for creation of a snakemake workflow using a singularity container on a hpc
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Some scripts for the methylation analysis of the ChickStress project.
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BARIC / Family Companion
CeCILL Free Software License Agreement v2.0Family-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
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Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variations detection.
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report from a BAM alignment the number of BX:Z: tags shared between to blocks of given size
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GenEpi / Tools / CpG island detection
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DUGAT-BONY Eric / Cheese_virome
Creative Commons Attribution Share Alike 4.0 InternationalUpdated -
bios4biol / intronSeeker
GNU General Public License v3.0 or laterUpdated -
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
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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.
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PAQmiR : Prediction Annotation and Quantification of miRNA with miRDeep2
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Martine Da-Rocha / CleaveLand_all_isomer
GNU General Public License v3.0 onlyModified 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.
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