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Institute of Botany of the Czech Academy of Sciences

Prague, Czech Republic

Simón Villanueva Corrales's starred repositories

Snaketool

Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff

Language:PythonMIT4300

goatools

Python library to handle Gene Ontology (GO) terms

Language:PythonBSD-2-Clause77100

syri

Synteny and Rearrangement Identifier

Language:CythonMIT32300

pycoQC

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

Language:PythonGPL-3.026000

pancat

Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions

Language:PythonAGPL-3.03100

applied-microeconometrics

Course website for Ph.D. Applied Microeconometrics at the KDI School.

Language:HTML11700

Rust

All Algorithms implemented in Rust

Language:RustMIT2226500

sucds

Collection of succinct data structures in Rust

Language:RustApache-2.08000

shshsh

a bridge between python and shell

Language:PythonMIT28300

reverse_argparse

A Python library to determine what exactly the user ran at the command line, along with default values, and any transformations that happened after parsing arguments.

Language:PythonBSD-3-Clause3800

HPP_Year1_Assemblies

Assemblies from HPP Year 1 production

6400

XAI-for-bioinformatics

Explainable AI for Bioinformatics

Language:Jupyter NotebookMIT11500

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonMIT27100

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

Language:PythonMIT335300

pyGenomeViz

A genome visualization python package for comparative genomics

Language:PythonMIT27300

SVDSS

Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)

Language:C++MIT4200

advent-of-code-rust

🎄Starter template for solving Advent of Code in Rust.

Language:RustMIT63100

gw

Genome browser and variant annotation

Language:C++MIT27000

aws-for-bioinformatics

AWS for Bioinformatics Researchers

Language:Jupyter NotebookApache-2.011700

teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

4600

functional-programming-jargon.py

Jargon from the functional programming world in simple terms!

MIT22900

charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.

Language:PythonNOASSERTION5200

yahs

Yet another Hi-C scaffolding tool

Language:CMIT12600

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Language:RMIT633100

enrichr_cli

Python script to use enrichr from command line (http://amp.pharm.mssm.edu/Enrichr/)

Language:Python700

flopp

flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.

Language:Rust3500

gfastats

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Language:C++MIT9100

csx46

Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University

Language:Jupyter NotebookApache-2.01400

gtfparse

Parsing tools for GTF (gene transfer format) files

Language:PythonApache-2.010900

bioframe

Genomic interval operations on Pandas DataFrames

Language:PythonMIT17300