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Adrien Leger's repositories

pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Language:PythonGPL-3.0249 5 98

NanoCount

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

Language:PythonMIT53 4 32

pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

Language:PythonGPL-3.034 7 25

NanopolishComp

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

Language:PythonMIT10 20

MetaCompore

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

Language:Python9 30

pycoSnake

pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data

Language:PythonMIT8 2 2

ContaVect

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

Language:PythonGPL-2.04 30

blastpy3

Simple and lightweight Python 3 wrapper module for NCBI BLAST+

Language:PythonGPL-3.03 20

JupyterGenoViewer

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

Language:Jupyter NotebookGPL-3.03 30

pyBioTools

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

Language:PythonGPL-3.03 20

Sekator

Multithreaded quality and adapter trimmer for PAIRED fastq files (Python2.7/Cython/C)

Language:PythonGPL-2.03 3 1

fastq_control_sampler

Generates control fastq files R1 and R2 from fasta reference sequences

Language:CGPL-3.02 3 1

Quade

Demultiplexer for PAIRED fastq files based on index sequence and PHRED quality (pure python)

Language:PythonGPL-2.02 30

DNA_photolitography_seq

Repository containing analyses and datasets

Language:HTMLMIT1 20

Fast5Tools

Tools to manipulate Fast5 files

Language:PythonGPL-3.01 20

nanocompore_paper_analyses

Analyses performed for the nanocompore paper

Language:Jupyter NotebookMIT1 30

pyDNA

Collection of python 2.7 Utilities and Wrapper for DNA / NGS data manipulation

Language:PythonGPL-2.01 20

versipy

Versatile version and medatada managment across the python packaging ecosystem with git integration

Language:PythonGPL-3.01 1 1

RefMasker

Hard mask homologies between fasta reference sequences identified by Blastn

Language:PythonGPL-2.0030

a-slide.github.io

My personal website powered by Publii and hosted by github pages

Language:HTML020

bioconda-recipes

Conda recipes for the bioconda channel.

Language:Shell010

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.

Language:Python020