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fnp_aux_scripts

Small scripts to help with fungal biosynthetic gene cluster mining

funcscan

Screening of functional components and natural products from assembled contigs

gecco

GEne Cluster prediction with COnditional random fields.

gecko

Toolbox for including enzyme constraints on a genome-scale model.

genegrouper

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

genomes-pipeline

MGnify genome analysis pipeline

get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

goatools

Python library to handle Gene Ontology (GO) terms

google-research

Google Research

gpt_protein_design

Efficient protein de novo design pipeline with GPT-based generator and transfer learning-based discrminator

graftm

GraftM - Rapid community profiles from metagenomes

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

hgtector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

humann

HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

integron_finder

Bioinformatics tool to find integrons in bacterial genomes

isdb

A database of In-Silico predicted MS/MS spectrum of Natural Products

isnv-calling

Bioinformatics pipeline for intrahost single nucleotide variation (iSNV) calling from viral genome deep sequencing data.

kaiju2-data-parser

keggcharter

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

kemet

KEGG Module Evaluation Tool

kemet-parser

kineticstools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

kofam_scan

CLI tool to annotate genes with KOfam

lcms2struct_exp

Scripts to run the experiments and analysis for the publication "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al.

localcolabfold

ColabFold on your local PC

longitudinal-notebooks

machine-learning-book

Code Repository for Machine Learning with PyTorch and Scikit-Learn

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

massbank-data

Official repository of open data MassBank records

massbank2db

Build a local SQLite Database from Massbank.