README.md

In travis-m-blimkie/TbTnseq: TnSeq pipeline functions by TB

TbTnseq

Description

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).

Dependencies

The only dependency is the tidyverse set of packages.

Workflow & Functions

• 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.

Installation

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)

travis-m-blimkie/TbTnseq documentation built on July 22, 2019, 7:39 a.m.