bioinformatics

OTP, One Touch Pipeline, Documentation at https://one-touch-pipeline.gitlab.io/otp/

SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.

For details on how to use and install visit the webpage

Armadillo: fast C++ library for linear algebra (matrix maths) & scientific computing - https://arma.sourceforge.net

Proteinortho is a tool to detect orthologous genes within different species. (Download)

CWL computational workflows

Travail réalisé durant mon stage de Master 2 Bio-informatique.

Unix toolkit for feature analysis of alternative splicing events. Includes basic functions for manipulating tables, extraction of exon and intron-related features, discriminate feature analysis, motif maps for RNA-binding proteins, and more.

Matlab toolbox to generate xTop intensities from peptide-level intensities. It can also generate TopPepN (N=1,2,3..) intensities. The most updated version is v2.0. A Python version of the code is present in version 1.2.

FFIND is a data-agnostic, scalable web platform with capability to integrate image and non-image data types (transcriptomics, flow cytometry, electrophysiology) into a user interface tailored to project-specific goals.

Nextflow pipeline for DamID analysis

Tavit (Trimming, Alignment and Variant Identification Tool) pipeline made in Python with Anaconda.

Bioinformatics in Python - DNA Toolkit YouTube Channel: https://t.ly/RdzG3

Run Oxford Nanopore MinION software in Docker containers

A d3 javascript SVG visualization of alternative splicing of randomly seeded exons from a random genome

This project includes python scripts with examples used for the below article in GBE. It is also archived on Figshare (https://doi.org/10.6084/m9.figshare.17111693).

Red algal plastids exhibit large genome size variation, especially in the recently described subphylum Proteorhodophytina. By contrast, their mitochondrial genomes remain unexplored. Here, we sequenced, assembled, and analyzed new plastid and mitochondrial genomes of 25 species of red microalgae. We uncovered new cases of genome size expansion in plastids and mitochondria, in both cases associated with group II intron proliferation. The phylogenomic analysis supported that these expansions occurred several times independently. URL: https://doi.org/10.1093/gbe/evac037

Colorful and fast BAM pileup.

A Ready-to-Use Virtual Machine for Teaching and Learning Bioinformatics

Python scripting for molecular dynamics simulation using GROMACS

Landing page of the DeePaC-F fungal database and models