The Ultimate Guide to the seeker Package in R

Explore valuable documentation and insights to make the most of the seeker package in R. Get ready to unlock the full potential of the seeker package!

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What is the seeker package?

In this section, we’ll delve into the fundamental aspects and key features of the package.

The seeker package aids in the search and retrieval of biological data from public databases. It includes several functions for querying, downloading, and managing data from major biological databases, making it an invaluable tool for research in the field of bioinformatics.

  • Title: Simplified Fetching and Processing of Microarray and RNA-Seq Data
  • Description: Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) , 'ArrayExpress' Kauffmann et al. (2009) , Robust multi-array average 'RMA' Irizarry et al. (2003) , and 'BrainArray' Dai et al. (2005) . For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger , performs quality control checks using 'FastQC' Andrews , quantifies transcript abundances using 'salmon' Patro et al. (2017) and potentially 'refgenie' Stolarczyk et al. (2020) , aggregates the results using 'MultiQC' Ewels et al. (2016) , maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) , and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) .
  • Author: Jake Hughey [aut, cre], Josh Schoenbachler [aut]
  • Maintainer: Jake Hughey

How to install the seeker package?

In this section, we’ll walk you through the process of installing and loading the seeker package. By following these steps, you can seamlessly add new functions, datasets, and other resources to your R environment for a more robust workflow.

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What package information should you know?

In this section, we’ll go over the technical aspects of the seeker package.

Key features

  • Datasets: Many R packages include built-in datasets that you can use to familiarize yourself with their functionalities. To identify built-in datasets. To identify the datasets for the seeker package, visit our database of R datasets.
  • Vignettes: R vignettes are documents that include examples for using a package. To view the list of available vignettes for the seeker package, you can visit our visit our database of R vignettes.
  • Citation: Citing R packages in your publications is important as it recognizes the contributions of the developers. To find citation information for the seeker package, visit our database of R package citations.

Technical details

  • License type: MIT + file LICENSE. For license details, visit the Open Source Initiative website.
  • Compilation requirements: Some R packages include internal code that must be compiled for them to function correctly. The seeker package does not have compilation requirements.
  • Required dependencies: A required dependency refers to another package that is essential for the functioning of the main package. The seeker package has the following required dependencies: R (>= 3.5).
  • Suggested dependencies: A suggested dependency adds extra features to the main package, but the main package can work without it. The seeker package has the following suggested dependencies: ArrayExpress (>= 1.62.0), Biobase, doParallel (>= 1.0.17), knitr, org.Mm.eg.db, rmarkdown, testthat (>= 3.1.0).
  • External dependencies: External dependencies are other packages that the main package depends on for linking at compile time. The seeker package does not use any external sources.
  • Imported packages: Importing packages allows developers to leverage existing code and functionalities without having to reinvent the wheel. The seeker package has the following imported packages: affy (>= 1.68.0), AnnotationDbi (>= 1.52.0), BiocManager (>= 1.30.0), biomaRt (>= 2.36.1), checkmate (>= 2.1.0), curl (>= 3.2), data.table (>= 1.11.8), foreach (>= 1.4.4), GEOquery (>= 2.58.0), glue (>= 1.5.0), jsonlite (>= 1.7.2), methods, qs (>= 0.21.2), R.utils (>= 2.11.0), RCurl (>= 1.98), readr (>= 1.4.0), sessioninfo (>= 1.2.0), tximport (>= 1.8.0), withr (>= 2.4.2), yaml (>= 2.2.1).
  • Enhancements: Enhancements help developers expand the capabilities of their packages without starting from scratch. The seeker package has no enhancements.

How to get help with the seeker package?

In this section, we’ll discuss a variety of available resources for getting help with the seeker package.

Key resources

  • The help() function: R’s built-in help system is a handy tool to find documentation. You can use the help("seeker") function to retrieve detailed information, examples, and usage instructions. Alternatively, you can use the ? operator as a shortcut.
  • Package website: The seeker package has a dedicated website. You can visit: https://seeker.hugheylab.org, https://github.com/hugheylab/seeker.
  • Developer support: You can email Jake Hughey . For contact information, visit our R community directory.

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