https://github.com/cmdoret/hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

bioinformatics genomics hi-c reproducibility

Last synced: 10 Apr 2025

https://github.com/cmdoret/tinycov

Command line tool to plot genomic coverage from a BAM file

coverage genomics-visualization rolling-windows

Last synced: 04 Aug 2025

https://github.com/cmdoret/dnaglider

Sliding window genome statistics on FASTA files

Last synced: 12 Jan 2026

https://github.com/cmdoret/clop

Last synced: 05 May 2025

https://github.com/cmdoret/acastellanii_genome_analysis

Comparative analysis of the genomes from two Acanthamoeba castellanii strains

Last synced: 13 Feb 2026

https://github.com/cmdoret/hic_scrambler

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

Last synced: 16 May 2025

https://github.com/cmdoret/acastellanii_legionella_infection

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

Last synced: 10 Oct 2025

https://github.com/cmdoret/acastellanii_genome_annotation

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

Last synced: 16 May 2025

https://github.com/cmdoret/mtg_ontology

An ontology describing cards in Magic The Gathering.

linkml mtg ontology rdf

Last synced: 15 Jun 2025

https://github.com/cmdoret/sequence_loopability

Investigating sequence features underlying chromatin loops

Last synced: 16 May 2025

https://github.com/cmdoret/master_archive

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

Last synced: 09 Sep 2025

https://github.com/cmdoret/acastellanii_hybrid_assembly

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

Last synced: 16 May 2025

https://github.com/cmdoret/yt2logseq

Experiment to generate logseq notes from a youtube video using ML.

logseq machine-learning note-taking video

Last synced: 08 Sep 2025

https://github.com/cmdoret/rdf-network-viz

Prefect workflow to visualize networks from RDF data

Last synced: 16 May 2025

https://github.com/cmdoret/dagws_seq_algo_materials

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

Last synced: 16 May 2025

https://github.com/cmdoret/vapormap

Cloud based pipeline for parallelized iterative alignment of Hi-C data

aws-batch genomics hi-c nextflow

Last synced: 23 Jan 2026

https://github.com/cmdoret/case_studies

Last synced: 25 Jan 2026

https://github.com/cmdoret/cmdoret.github.io

My personal website

Last synced: 10 Feb 2026

https://github.com/cmdoret/misc_scripts

These are various scripts I wrote for fun.

Last synced: 30 Oct 2025

https://github.com/cmdoret/dotfiles

collection of configuration files

Last synced: 02 Mar 2026

https://github.com/cmdoret/jigsaw-toxic-comment-classification-challenge-2018

Improving best solutions from an old competition for educational purpose

Last synced: 25 Jan 2026

https://github.com/cmdoret/nixos

get nixxed 🧊

Last synced: 25 Jun 2025

https://github.com/cmdoret/cmdoret

Last synced: 24 Jan 2026

https://github.com/cmdoret/test_snakemake_kubernetes

minimal example with snakemake + gcloud + kubernetes

Last synced: 15 Oct 2025

https://github.com/cmdoret/archive_first_step

Last synced: 05 Feb 2026

https://github.com/cmdoret/strangerseq

Generate DNA sequences minimizing microhomology

dna-sequences genomics k-mer

Last synced: 05 Oct 2025

https://github.com/cmdoret/data_analysis

Reports for the advanced data analysis class

Last synced: 16 May 2025

https://github.com/cmdoret/htslurp

slurp noodles-htsget streams into python

Last synced: 16 May 2025

https://github.com/cmdoret/game_of_life

A small game written in python we made for a school project.

Last synced: 17 Sep 2025