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Simón Villanueva Corrales (sivico26)

sivico26

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Company:Institute of Botany of the Czech Academy of Sciences

Location:Prague, Czech Republic

Twitter:@Sivico26

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Simón Villanueva Corrales's starred repositories

Rust

All Algorithms implemented in Rust

Language:RustLicense:MITStargazers:21126Issues:228Issues:68

FriendsDontLetFriends

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

Language:RLicense:MITStargazers:6154Issues:104Issues:7

pomegranate

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

Language:PythonLicense:MITStargazers:3283Issues:96Issues:770

goatools

Python library to handle Gene Ontology (GO) terms

Language:PythonLicense:BSD-2-ClauseStargazers:734Issues:23Issues:210

advent-of-code-rust

🎄Starter template for solving Advent of Code in Rust.

Language:RustLicense:MITStargazers:623Issues:7Issues:26

syri

Synteny and Rearrangement Identifier

Language:CythonLicense:MITStargazers:298Issues:5Issues:244

shshsh

a bridge between python and shell

Language:PythonLicense:MITStargazers:284Issues:3Issues:2

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonLicense:MITStargazers:268Issues:5Issues:12

pycoQC

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

Language:PythonLicense:GPL-3.0Stargazers:245Issues:5Issues:97

pyGenomeViz

A genome visualization python package for comparative genomics

Language:PythonLicense:MITStargazers:242Issues:3Issues:29

functional-programming-jargon.py

Jargon from the functional programming world in simple terms!

License:MITStargazers:227Issues:4Issues:0

bioframe

Genomic interval operations on Pandas DataFrames

Language:PythonLicense:MITStargazers:167Issues:13Issues:105

gw

Genome browser and variant annotation

Language:C++License:MITStargazers:146Issues:2Issues:12

applied-microeconometrics

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

Language:HTMLStargazers:113Issues:4Issues:0

yahs

Yet another Hi-C scaffolding tool

Language:CLicense:MITStargazers:110Issues:6Issues:89

aws-for-bioinformatics

AWS for Bioinformatics Researchers

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:110Issues:7Issues:0

gtfparse

Parsing tools for GTF (gene transfer format) files

Language:PythonLicense:Apache-2.0Stargazers:108Issues:7Issues:22

XAI-for-bioinformatics

Explainable AI for Bioinformatics

Language:Jupyter NotebookLicense:MITStargazers:108Issues:4Issues:0

gfastats

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

Language:C++License:MITStargazers:86Issues:5Issues:20

sucds

Collection of succinct data structures in Rust

Language:RustLicense:Apache-2.0Stargazers:79Issues:7Issues:15

HPP_Year1_Assemblies

Assemblies from HPP Year 1 production

Stargazers:63Issues:16Issues:2

charcoal

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

Language:PythonLicense:NOASSERTIONStargazers:49Issues:19Issues:163

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.

Stargazers:45Issues:5Issues:0

SVDSS

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

Language:C++License:MITStargazers:40Issues:4Issues:20

awesome-conformal-prediction

A professionally curated list of awesome Conformal Prediction videos, tutorials, books, papers, PhD and MSc theses, articles and open-source libraries.

License:CC0-1.0Stargazers:37Issues:1Issues:10

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:PythonLicense:NOASSERTIONStargazers:36Issues:4Issues:37

flopp

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

Language:RustStargazers:33Issues:3Issues:18

pancat

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

Language:PythonLicense:AGPL-3.0Stargazers:31Issues:2Issues:14

csx46

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

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:14Issues:0Issues:0

enrichr_cli

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

Language:PythonStargazers:7Issues:0Issues:0