DuffyTools: Duffy Lab "Tools" package Overview
In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

DuffyTools

R Documentation

Duffy Lab "Tools" package Overview

Description

A suite of R tools from the lab of Patrick Duffy, providing a common infrastucture for our microarray (DuffyMA), NextGen sequencings (DuffyNGS), and proteomics (DuffyProteome) packages.

Details

This package provides a variety of utilities and data manipulation functions that are common to the Duffy Lab's R packages for functional genomics spanning the domains of microarrays (DuffyMA), next gen sequencing (DuffyNGS), and proteomics (DuffyProteome).

Primary focus is on providing a universal and flexible method of working with genomic feature annotations, from any number of organisms, in a user controllable format. This allows for transcriptional studies of organisms with evolving annotations, such as many pathogens and parasites. Further, the platform is explicitly designed for mixed-organism data collection platforms such as microarrays with both host and parasite probes, or RNA-seq of mixed genetic material such as field samples drawn from infected individuals.

For details about annotations, including adding new organism definitions or customizing existing annotations, see MapSets. For details about setting the target organism(s) for analysis, including adding new mixed-organism capabilities, see Targets. For details on switching between organisms (species) during analysis, see Species.

A second major focus is on tools that produce and operate on transcription and differential expression (DE) data sets. Utilities supporting operations such as clustering, plotting, and comparisons are included. Methods for detecting DE genes based on Round Robin, Rank Product, EdgeR, DESeq, and SAM, are supported.

To support this focus, the package tries to migrate as many user settable parameters as feasible into configuration files that are local to each experiment. By convention, we divide these parameters into 2 categories: ones that can be thought of as sample specific are found in an AnnotationTable, and ones that are common to the entire experiment are found in an OptionsTable. In this manner, much of the behavior of the lab's functional genomics packages can be customized by the end user without altering the underlying R code.

This package also includes a variety of functions for mathematic operations, file manipulation in general, and specific tools for FASTA and FASTQ formats. Lastly, any other tools that are generic enough to be shared by our functional genomics packages tend to be thrown into the DuffyTools package.