Extended Data Fig. 1: RB-TnSeq R data processing pipeline for gene fitness comparison across multiple conditions.
From: Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness
The pipeline is divided into three main scripts. Script 1 calculates the normalized gene fitness for each replicate of an RB-TnSeq experiment. This script has to be run for each replicate independently. Then, the .Rdata files from Script 1 are loaded in Script 2. Script 2 calculates for each RB-TnSeq condition the average gene fitness across replicates (inverse-variance weighted average). Finally, Script 3 compares gene fitness values of each RB-TnSeq condition against a chosen reference condition.