Teaching
Medical microbiological diagnosis
An interactive Microbiology I course material, from specimen to result, with simulators, cases and self-assessment.
HTMLSVGJavaScript
Infectious Disease Epidemiology Active
Tools / Methods
Methodological tools
Statistical, epidemiological, and predictive methods developed by the research group in R and Python to support clinical decision-making and population-level analysis.
Methods and applications
Tools of the Research Group
Statistical
Evidence-based physical diagnosis
A finder for physical examination signs with their measured diagnostic performance.
PythonJavaScriptPubMedCrossref
Clinical, Epidemiological, and Translational Active
Teaching
VIROLOGY
An active-learning tool for medical virology.
HTMLSVGJavaScript
Infectious Disease Epidemiology Active
Statistical
Bayesian WISCA
Weighted-incidence syndromic combination antibiograms (WISCA) with Bayesian modeling — the right antibiotic from the first dose.
RbrmsStanHTMLJavaScript
Infectious Disease Epidemiology Active
Predictive
Dengue Forecast
Probabilistic dengue forecasting and early warning for all 32 states of Mexico.
RGradient boostingBayesianConformal prediction
Infectious Disease Epidemiology Beta
Pipeline
Microbial genomics pipeline (WGS)
Assembly, typing, and genotypic resistance from sequencing data.
NextflowSPAdesABRicatePython
Molecular Biology and Biomarkers Active
Statistical
Epidemiological time series
Disease trends, seasonality, and the reproduction number.
REpiEstimforecast
Population Data Science Active
Statistical
Spatial analysis and population-level determinants
Spatial autocorrelation and determinants at the municipal scale.
Rsfspdep
Population Data Science In development
Stack R · Python · Stan / brms · sf · spdep · EpiEstim · Nextflow · tidyverse
Section · Clinical laboratory
Laboratory
“Del tubo al diagnóstico” (From the tube to the diagnosis) series: a biomarker reference, reference intervals and result verification for clinical chemists, quality managers and physicians. They run in the browser and the data you enter never leave your device. Content is in Spanish.
Open the section index →Reference
From the tube to the diagnosis: a 60-biomarker reference
What each marker is, which tube it is drawn in, how it is stored and measured, why it rises or falls and how it is interpreted.
HTMLJavaScriptCLSIEFLM
Clinical, Epidemiological, and Translational Active
Statistical
Reference intervals: verify, establish and transfer
Does the package-insert interval fit my population and my method? How do I build my own?
JavaScriptCLSI EP28Harris–BoydrefineR
Population Data Science Active
Statistical
Delta check: comparing the patient with themself
Is this change between two results from the same patient real, an error or noise? Which limit and which window to use.
JavaScriptCLSI EP33EFLMRCV
Clinical, Epidemiological, and Translational Active
Section · Open Biostatistics
Open Biostatistics
Explained calculators for clinical research: each one shows the classic equation, a plain explanation, a plain-language interpretation, the equivalent R code and the original sources. Compute, understand, cite. Your data never leave the browser.
Open the section index →Statistical
Open Biostatistics: diagnostic tests
Sensitivity, specificity, predictive values and likelihood ratios from a 2×2 table; post-test probability with Fagan's nomogram.
TypeScriptRwebR
Clinical, Epidemiological, and Translational Beta
Statistical
Open Biostatistics: association and effect in 2×2 tables
Relative risk, odds ratio, absolute risk reduction and NNT; chi-squared, Fisher's exact test and McNemar.
TypeScriptRwebR
Clinical, Epidemiological, and Translational Beta
Statistical
Open Biostatistics: sample size and power
Estimate a proportion or a mean, compare two proportions or two means, diagnostic precision (Buderer) and correlation, with power curves.
TypeScriptRwebR
Clinical, Epidemiological, and Translational Beta
Statistical
Open Biostatistics: agreement and descriptive statistics
Cohen's kappa, CI for a proportion (six methods) and for a mean, mean and SD from the median, descriptive statistics with a chart.
TypeScriptRwebR
Clinical, Epidemiological, and Translational Beta
Statistical
Open Biostatistics: regression and survival models
Logistic regression, Cox, Kaplan-Meier with log-rank and linear regression, with real R running in the browser (webR).
TypeScriptRwebR
Clinical, Epidemiological, and Translational Beta