Pinned Repositories
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
MetaCompore
Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing
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
pycoMeth
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
pycoQC
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
pycoSnake
pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data
Sekator
Multithreaded quality and adapter trimmer for PAIRED fastq files (Python2.7/Cython/C)
versipy
Versatile version and medatada managment across the python packaging ecosystem with git integration
a-slide's Repositories
a-slide/pycoQC
pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
a-slide/NanoCount
EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
a-slide/pycoMeth
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
a-slide/NanopolishComp
NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files
a-slide/MetaCompore
Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing
a-slide/pycoSnake
pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data
a-slide/ContaVect
Complete suite to analyse DNA contaminants of virus/vector preparation from NGS data
a-slide/blastpy3
Simple and lightweight Python 3 wrapper module for NCBI BLAST+
a-slide/JupyterGenoViewer
JGV is a Python3 package for an embed genomic viewer in Jupyter notebook
a-slide/pyBioTools
Collection of tools to manipulate Bioinformatic standard file format + Generic file related function collection
a-slide/Sekator
Multithreaded quality and adapter trimmer for PAIRED fastq files (Python2.7/Cython/C)
a-slide/fastq_control_sampler
Generates control fastq files R1 and R2 from fasta reference sequences
a-slide/Quade
Demultiplexer for PAIRED fastq files based on index sequence and PHRED quality (pure python)
a-slide/DNA_photolitography_seq
Repository containing analyses and datasets
a-slide/Fast5Tools
Tools to manipulate Fast5 files
a-slide/nanocompore_paper_analyses
Analyses performed for the nanocompore paper
a-slide/pyDNA
Collection of python 2.7 Utilities and Wrapper for DNA / NGS data manipulation
a-slide/versipy
Versatile version and medatada managment across the python packaging ecosystem with git integration
a-slide/RefMasker
Hard mask homologies between fasta reference sequences identified by Blastn
a-slide/a-slide
a-slide/a-slide.github.io
My personal website powered by Publii and hosted by github pages
a-slide/bioconda-recipes
Conda recipes for the bioconda channel.
a-slide/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.
a-slide/FastqSweeper
Simple python pipeline to clean fastq files with cutadapt and bwa substractive mapping
a-slide/Jupyter_Rise_Presentations
a-slide/nanocompore_pipeline
Nextflow pipeline for nanocompore analysis
a-slide/presentation_repo
a-slide/pycltools
python3 library containing general utilities to manipulate files, strings and folders
a-slide/singularity
Repository with my singularity recipes hosted at Singularity Hub
a-slide/TaqMDA
Multi-dimensional analyse for RT QPCR data obtained from Taqman QPCR arrays