cmdoret

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

tinycov

Command line tool to plot genomic coverage from a BAM file

mtg_ontology

An ontology describing cards in Magic The Gathering.

clop

dnaglider

Sliding window genome statistics on FASTA files

Acastellanii_genome_analysis

Comparative analysis of the genomes from two Acanthamoeba castellanii strains

Acastellanii_genome_annotation

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

Acastellanii_legionella_infection

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

HiC_scrambler

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

Acastellanii_hybrid_assembly

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

cmdoret.github.io

My personal website

genome_assembly_tools

List of genome assembly tools

rdf-network-viz

Prefect workflow to visualize networks from RDF data

sequence_loopability

Investigating sequence features underlying chromatin loops

yt2logseq

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

calamus

A JSON-LD Serialization Libary for Python

catplus-chembord

Frontend for the Catplus project

causalimpact

Python port of CausalImpact R library

cmdoret

digiplant

dotfiles

collection of configuration files

HiC_reassembler

HiCExperiment

htslurp

slurp noodles-htsget streams into python

maturin-nix-example

nixos

get nixxed 🧊

phd

My PhD thesis and associated manuscripts

renku

The Renku Project provides a platform and tools for reproducible and collaborative data analysis.

renku-project-template

A repository for default Renku project templates.

renku-python

A Python library for the Renku collaborative data science platform.