pathogens

CDCgov/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

cmmr/EsViritu

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

bacpop/mandrake

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

ncrna/PathogenTrack

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Gibbons-Lab/isb_course_2023

Materials and presentation for the 2023 ISB Microbiome course.

AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

mattmar/dynamAedes

Model to simulate the population dynamics of four Aedes mosquito species.

Camilo-Mora/Diseases

Systematic assessment of the impacts of climate change on human pathogenic diseases

trypanosomatics/aprank

This is APRANK, an Antigenic Protein and Peptide Ranker.

usegalaxy-eu/PathoGFAIR

PathoGFAIR: Galaxy FAIR Workflows for Pathogen Detection and Samples Comparison

ComputationalBiologyLab/AntiPan

Comprehensive in-silico subunit vaccine discovery workflow

duncanberger/PZQ_POPGEN

Code repository for the publication: "Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration"

Julio92-C/hosMicro

An interactive and user-friendly web application to explore the hospital microbiome and genetic makeup

dendrologicus/Dcoronariae_Popgen

Multiplexed SSR marker analysis of Diplocarpon coronariae reveals clonality within samples from Middle Europe and genetic distance from Asian and North American isolates

dendrologicus/PRRC_qPCR_T18

Untangling the pea root rot complex leads to the identification of microbial markers for plant health

emdelponte/pyblastr

Tracking the movement of cereal blast caused by Pyricularia

sib-swiss/hugo-pathogens-portal

Hugo pathogens portal theme

tznurmin/TEA_curated_data

Curated data and source articles for microbial strains (Strain Tagger) and human microbial pathogens (Pathogen Identifier) datasets. Over 3,500 tagged entities from hundreds of full-length articles.

ANSES-Ploufragan/PrepMedVet_MinION

galaxy wf detect pathogens in MinION data

ccdmb/PathoPore

PathoPore - Longer Sequences and NextFlow Faster Analysis

duncanberger/SM_VARIATION

Code repository for the manuscript: Extensive transmission and variation in a functional receptor for praziquantel resistance in endemic Schistosoma mansoni

psasickness/psasickness.github.io

ShwetaNagre/MIP_ORACLE

MIP_ORACLE: Identifies unique target regions with diagnostic significance in pathogens.

skuthyar/Colonization_resistance

Code for analyzing qPCR and 16S data from microbiome-mediated resistance experiments done in vitro

ttmgr/Wetland_Health

This project investigates the microbial and viral communities, vertebrate biodiversity, and prevalence of antimicrobial resistance (AMR) genes in 12 European wetlands across Germany, France, and Spain

akarazeev/LauzHack19

🇨🇭🦠 Service for pathogens and threats identification in hospital environments - SOPHiA Genetics

pmoris/FiMAB-bioinformatics

Course on bioinformatics (linux intro + DNA sequencing pipeline) for the Fighting Malaria Across Borders training programme by the Institute of Tropical Medicine and VLIR-UOS (Belgium)