a-slide

a-slide.github.io

My personal website powered by Publii and hosted by github pages

bash_ngs_tools

Collection of simple NGS tools

bioconda-recipes

Conda recipes for the bioconda channel.

blastpy3

Simple and lightweight Python 3 wrapper module for NCBI BLAST+

bsub_jupyter

Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.

chimera_finder

These BASH script allow to extract chimeric pairs and chimeric reads from NGS data mixing 2 DNA references

contavect

Complete suite to analyse DNA contaminants of virus/vector preparation from NGS data

dna_photolitography_seq

Repository containing analyses and datasets

fast5tools

Tools to manipulate Fast5 files

fastq_control_sampler

Generates control fastq files R1 and R2 from fasta reference sequences

fastqsweeper

Simple python pipeline to clean fastq files with cutadapt and bwa substractive mapping

find_overlap_reads

Parse a BAM file and extract reads ovelapping given genomic coordinates

generateur_genotypes

Entrée = taille de génotype/haplotype + nombre d'haplotype + nombre de génotype + nombre d’ambiguïté max/ genotype Sortie = fichier contenant une liste de génotype + fichier "solution" contenant la même liste de génotype, mais avec les haplotypes à l'origine intercalés

haplotype_inference

Projet TP algo

ipython-notebook

Repo to store my iPython notebooks for NGS data analases

isfinder

IsFinder find virus insertion site in host genomic DNA from pair end NGS data

isis

ISIS generates random insertion sites of a given viral DNA in an host DNA and output Fastq Files

jupyter_rise_presentations

jupytergenoviewer

JGV is a Python3 package for an embed genomic viewer in Jupyter notebook

metacompore

Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

mirstat

Simple tool to analyze miRNA QPCR data

nanocompore_paper_analyses

Analyses performed for the nanocompore paper

nanocompore_pipeline

Nextflow pipeline for nanocompore analysis

nanocount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

nanopolishcomp

NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

presentation_repo

pybioplot

High level library for Python 3 containing functions to generate specific plot for NGS and other biology related datasets.

pybiotools

Collection of tools to manipulate Bioinformatic standard file format + Generic file related function collection

pybioutil

High level library for Python 3 containing functions for data analysis of NGS and other biology related datasets.