CAFE-R

CAFE-R analyzes transposon insertion sequencing (Tn-seq) paired-sample data to compute gene-level fitness coefficients and assess differential mutant fitness across conditions.

Key Features:

• Paired-Sample Analysis: Handles paired experimental comparisons to quantify differential fitness between conditions using transposon insertion sequencing data.
• Fitness Coefficient Calculation: Computes fitness coefficients for each gene based on read enrichments to quantify the impact of transposon insertions.
• Statistical Testing: Performs statistical tests on fitness coefficients to identify significant differences in mutant fitness.
• Implementation in R and Perl: Implemented using R and Perl for the computational analyses.

Scientific Applications:

• Microbial genetics: Large-scale analysis of transposon mutant libraries to characterize gene function in microbes.
• Functional genomics: Systematic assessment of gene fitness across conditions to map genotype–phenotype relationships.
• Essential gene and interaction discovery: Identification of essential genes and genetic interactions through differential fitness measurements.

Methodology:

Performs paired-sample analysis of transposon insertion sequencing read enrichments to calculate gene-level fitness coefficients and applies statistical testing; implemented in R and Perl.