Seroanalytics

A directory of free, open-source tools for exploring, modeling and understanding serological data.

GitHub Docker Hub

How to Use Seroanalytics

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Simulate
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Visualise
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Model

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Simulate

Generate synthetic serological data for testing and validation

serosim logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

serosim is an R package for simulating serological data from user-specified vaccine or infection-generated and antibody kinetics processes.

Web App Documentation DOI GitHub

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Visualise

Create compelling visualizations of serological data

seroviz logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

SeroViz is an online tool for visualising surveillance and exposure data. Scale and disaggregate, fit splines, and download plots.

Web App GitHub

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Model Cross-Sectional Data

Analyze cross-sectional serological data with advanced statistical models

Rsero Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

Rsero is an R package to estimate the annual force of infection using serological data. It provides tools for analyzing cross-sectional serological surveys and fitting serocatalytic models.
External package - not managed by seroanalytics

Documentation DOI GitHub

serofoi logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

serofoi is an R package to estimate the Force-of-Infection (FoI) of a given pathogen from age-disaggregated population-based cross-sectional serosurveys, using a Bayesian framework. Part of the Epiverse Initiative.
External package - not managed by seroanalytics

Documentation GitHub

serosv logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

serosv is an easy-to-use and efficient tool to estimate infectious diseases parameters (seroprevalence and force of infection) using serological data.
External package - not managed by seroanalytics

Documentation GitHub

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Model Longitudinal Data

Track antibody kinetics and immune responses over time

serosolver Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

serosolver is an R package using a hierarchical model with a custom Markov chain Monte Carlo sampler to simultaneously infer antibody kinetics and infection histories from cross-sectional or longitudinal serological data.

Documentation DOI GitHub

epikinetics Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

epikinetics is an R package for Bayesian hierarchical modelling of antibody kinetics.

Documentation GitHub

serojump logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

serojump is an R package providing tools for fitting serological models to antibody kinetics data using reversible-jump Markov Chain Monte Carlo (RJ-MCMC).

Web App Documentation DOI GitHub

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Other

Additional tools for serological analysis

SeroMetrics Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

An R package designed to quantify an individual’s antigenic landscape, which comprises hemagglutination inhibition (HAI) titers against a panel of influenza viruses isolated at various times or in different antigenic spaces.
External package - not managed by seroanalytics

Documentation GitHub

serocalculator Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

Provides a rapid and computationally simple method for calculating seroconversion rates
External package - not managed by seroanalytics

Documentation GitHub

seroCOP logo Project Status: Active – The project has reached a stable, usable state and is being actively developed. GitHub last commit

R package for analyzing correlates of protection using Bayesian methods.

Web App Documentation GitHub