The LeadDiscoveryDocking pipeline is designed for high-throughput screening, scoring, and refinement of small molecule leads for protein-ligand docking.

"Your Fully-Automated Personal AI Assistant, and Open-Source & Cost-Efficient Alternative to OpenAI's Deep Research"

LLM based autonomous agent that conducts deep local and web research on any topic and generates a long report with citations.

An AI-powered research assistant that performs iterative, deep research on any topic by combining search engines, web scraping, and large language models. The goal of this repo is to provide the si…

Single species bacterial isolate genomic analysis

Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

AMR/VF LGT focused bacterial genomics analysis workflow

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

Detection of pseudogene candidates in bacterial and archaeal genomes.

Main scripts and utility scripts used for the paper "Clinical characteristics and pre-existing genetic variation determine some adaptive strategies employed by Staphylococcus aureus strains during …

An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations.

Repository related to main pipeline in Within Host Adaptation paper (Gatt and Margalit, Mol Biol Evol, in review)

Repository to Hold Code base for 'The Intra-Host Evolutionary Landscape And Pathoadaptation Of Persistent Staphylococcus aureus In Chronic Rhinosinusitis' Paper

Condense and summarize many results form ISEScan into CSV for heatmaps

Suporting code for manuscript: "Beyond to the stable: role of the insertion sequences as epidemiological descriptors in Corynebacterium striatum"

A set of scripts for calculating pairwise SNP distance

Scripts to extract information from trees and tree distributions

R code to extract KEGG pathways numbers present in prokaryotes, and therefore exclude those from Ekaryotes

Genome-scale protein function classification

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

An analysis and visualization platform for 'omics data

A tooL for Prokaryotic Phylogeny And Clustering Analysis

This is a chewBBACA-generated cgMLST scheme used for typing Klebsiella aerogenes complex (KAC) species to clonal cluster (CC) level.

Python package for AutoML on Tabular Data with Feature Engineering, Hyper-Parameters Tuning, Explanations and Automatic Documentation

AutoScore: An Interpretable Machine Learning-Based Automatic Clinical Score Generator

hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance