This package was removed from CRAN on 2025-02-11. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.1.6, its last release before removal.

seeker

1.1.6

Simplified Fetching and Processing of Microarray and RNA-Seq Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Jake Hughey10 releasesCRAN page ↗GitHub ↗

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) doi:10.1093/bioinformatics/btm254, 'ArrayExpress' Kauffmann et al. (2009) doi:10.1093/bioinformatics/btp354, Robust multi-array average 'RMA' Irizarry et al. (2003) doi:10.1093/biostatistics/4.2.249, and 'BrainArray' Dai et al. (2005) doi:10.1093/nar/gni179. 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 https://github.com/FelixKrueger/TrimGalore, performs quality control checks using 'FastQC' Andrews https://github.com/s-andrews/FastQC, quantifies transcript abundances using 'salmon' Patro et al. (2017) doi:10.1038/nmeth.4197 and potentially 'refgenie' Stolarczyk et al. (2020) doi:10.1093/gigascience/giz149, aggregates the results using 'MultiQC' Ewels et al. (2016) doi:10.1093/bioinformatics/btw354, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) doi:10.1038/nprot.2009.97, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) doi:10.12688/f1000research.7563.2.

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/seeker/seeker_1.1.6.tar.gz"
pkgFile <- "seeker_1.1.6.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1.6) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("hugheylab/seeker")

Development version from hugheylab/seeker. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-seeker

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.46

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 94%
Return-value docs: 100%
References docs: 0%

Downloads

seeker Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on75 r2u

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (20)

affy AnnotationDbi BiocManager (>= 1.30.0)biomaRt checkmate curl (>= 3.2)data.table foreach GEOquery (>= 2.58.0)glue jsonlitemethodsqs (>= 0.21.2)R.utils RCurl readr (>= 1.4.0)sessioninfo tximport withr (>= 2.4.2)yaml

LinkingTo (0)

none

Suggests (7)

ArrayExpress Biobase doParallel knitr org.Mm.eg.db rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Jake Hughey

Author, Maintainer

Authors (2)

Jake Hughey

Author, Maintainer

Josh Schoenbachler

Author

Package Timeline

10 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-02-11
issues were not corrected in time
1.1.6
2024-08-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.5
2024-01-22 · diff ↗
1.1.4
2023-12-04 · diff ↗
1.1.3
2023-05-23 · diff ↗
1.1.2
2023-05-17 · diff ↗
1.1.1
2023-05-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
2023-03-22 · diff ↗
1.0.13
2022-10-20 · diff ↗
1.0.10
2022-09-19 · diff ↗
1.0.9
2022-08-09
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 10
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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