cmdoret/cmdoret.github.io

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cmdoret/cmdoret.github.io

cmdoret

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My personal website

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

tinycov

Command line tool to plot genomic coverage from a BAM file

Acastellanii_genome_analysis

Comparative analysis of the genomes from two Acanthamoeba castellanii strains

HiC_scrambler

Introducing structural variations in Hi-C contact maps to try detecting and reversing them.

dnaglider

Sliding window genome statistics on FASTA files

Acastellanii_legionella_infection

Analysis of genomic changes induced in Acanthamoeba castellanii C3 following infection by Legionella pneumophila

Acastellanii_genome_annotation

Reproducible container-based pipeline for the annotation of the Acanthamoeba castellanii genome

rdf-network-viz

Prefect workflow to visualize networks from RDF data

Jupyter Notebook

dagws_seq_algo_materials

Slides and exercises from the "Sequence Algorithms" lectures I gave for the data analysis in genomics (DAG) workshop.

Jupyter Notebook

sequence_loopability

Investigating sequence features underlying chromatin loops

Jupyter Notebook

master_archive

Master project for the Molecular Life Sciences master in Bioinformatics, University of Lausanne

CSD_Lfabarum

Genomics pipeline to reproduce the analysis from Matthey-Doret et al., 2019, Genome Biology and Evolution

Acastellanii_hybrid_assembly

Hybrid genome assembly of Acanthamoeba castellanii. Combining long reads, Hi-C and shotgun.