Matteopaluh

rembg

Rembg is a tool to remove images background

data-engineer-handbook

This is a repo with links to everything you'd ever want to learn about data engineering

stat_rethinking_2022

Statistical Rethinking course winter 2022

camelot

A Python library to extract tabular data from PDFs

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

R-graph-gallery

A website that displays hundreds of R charts with their code

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

ffq

A tool to find sequencing data and metadata from public databases.

DeepFRI

Deep functional residue identification

CLEAN

CLEAN: a contrastive learning model for high-quality functional prediction of proteins

mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling

plass

sensitive and precise assembly of short sequencing reads

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

SemiBin

SemiBin: metagenomics binning with self-supervised deep learning

enrichM

Toolbox for comparative genomics of MAGs

aviary

A hybrid assembly and MAG recovery pipeline (and more!)

GenoVi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake

MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

GenomeSPOT

Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome

ModelSEEDpy

Python package for building and analyzing models using ModelSEED

UniFuncNet

A multi-reference network annotation tool to support omics analysis

emapper2gbk

Convert GFF, fastas, annotation table and species name into Genbank.

OrthOmics

Collection of scripts for gene age sorting and multi-omics data mining and analysis

GTDB2DIAMOND

Set of simple auxiliary python scripts to help create GTDB databases for annotation with DIAMOND

bayesian_statistics_for_computational_biology

A Bayesian statistics course for computational biologists

coco_paper

Casini_2022_GEM

Supplementary scripts of Casini, I., et al. "An integrated systems-biology platform for power-to-gas technology"

VisomX

An R package for User-Friendly and Comprehensive Analysis and Visualization of Omics Data

FermentationExplorer

🧪A resource for showing the incredible diversity of fermentative metabolism