Analysis of Microbial Social Behavior in Bacterial Consortia.

bsocialv2

Analysis of Microbial Social Behavior in Bacterial Consortia

Overview

bsocialv2 provides an S4 class and methods for analyzing microbial social behavior in bacterial consortia. The package implements a complete analysis pipeline:

1. Data Import - Raw plate reader data or pre-processed growth parameters
2. Growth Analysis - Parameter extraction (NGen, GR, LogPhase) via growthcurver or grofit
3. Social Behavior - Fitness comparisons identifying cooperators, cheaters, and neutrals
4. Diversity Effects - Relationship between consortium diversity and fitness
5. Stability Analysis - Coefficient of variation across replicates/diversity levels
6. Assembly Paths - Graph-based consortium assembly sequence finding

Installation

# Install from GitHub
remotes::install_github("Juane99/bsocialv2")

# Or install from CRAN (once accepted)
# install.packages("bsocialv2")

Quick Start

library(bsocialv2)

# Create a bsocial object
obj <- new("bsocial")

# Load your data
consortia <- read.csv("consortia.csv")
curated <- read.csv("curated_data.csv")

obj@cepas_seleccionadas <- setdiff(colnames(consortia), "Consortia")
obj@datos_crudos <- list(
  consortia = consortia,
  curated = curated,
  type = "curated"
)

# Run the analysis pipeline
obj <- transform_curated_data(obj)
obj <- analyze_growth(obj)
obj <- analyze_social_behavior(obj)
obj <- summarize_social_behavior(obj)
obj <- analyze_diversity(obj)
obj <- analyze_stability(obj)
obj <- analyze_biofilm_sequence(obj)

# Access results
obj@graficos$growth_scatter
obj@resultados_analisis$summary_gen

See vignette("bsocial-workflow") for a complete tutorial.

License

MIT.