R package for running a TnSeq essentiality analysis pipeline. Designed for use with raw TnSeq results from Tradis and Transit (Gumbel) to produce a list of essential genes. Allows the specification of stringency threshold in relation to the number of replicates (e.g. for Tradis, a gene is essential if it has 0 counts in at least 2 of 3 replicates).
The only dependency is the tidyverse set of packages.
- tbt_readFiles: Read in files produced by Tradis or Transit/Gumbel and select appropriate columns, namely gene name and columns denoting essentiality (Read Counts for Tradis, Call for Transit/Gumbel)
- tbt_rename: Renames count or call column to be unique for each replicate in a given condition/treatment (user-defined).
- tbt_essential: Return a data frame of essential genes for Tradis or Transit/Gumbel.
The simplest way to intsall the package is through the devtools::install_github() function. One can simply copy and paste the code below into the RStudio console to install and load the package:
devtools::install_github("travis-m-blimkie/TbTnseq")
library(TbTnseq)