Other packages > Find by keyword >

seeker  

Simplified Fetching and Processing of Microarray and RNA-Seq Data
View on CRAN: Click here


Download and install seeker package within the R console
Install from CRAN:
install.packages("seeker")

Install from Github:
library("remotes")
install_github("cran/seeker")

Install by package version:
library("remotes")
install_version("seeker", "1.1.6")



Attach the package and use:
library("seeker")
Maintained by
Jake Hughey
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-08-09
Latest Update:
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) .
How to cite:
Jake Hughey (2022). seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data. R package version 1.1.6, https://cran.r-project.org/web/packages/seeker. Accessed 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:02), 1.0.9 (2022-08-09 15:00), 1.0.10 (2022-09-20 01:06), 1.0.13 (2022-10-20 08:40), 1.1.0 (2023-03-22 09:40), 1.1.1 (2023-05-05 18:00), 1.1.2 (2023-05-17 23:40), 1.1.3 (2023-05-24 01:40), 1.1.4 (2023-12-04 08:10), 1.1.5 (2024-01-22 19:50), 1.1.6 (2024-08-27 05:50)
Other packages that cited seeker R package
View seeker citation profile
Other R packages that seeker depends, imports, suggests or enhances
Complete documentation for seeker
Functions, R codes and Examples using the seeker R package
Some associated functions: checkDefaultCommands . fastqc . fastqscreen . fetch . fetchMetadata . getPlatforms . getSalmonMetadata . getTx2gene . installCustomCdfPackages . installSysDeps . multiqc . salmon . seeker . seekerArray . trimgalore . tximport . 
Some associated R codes: array.R . array_utils.R . fetch.R . install_sys_deps.R . qc.R . salmon.R . seeker.R . tximport.R . utils.R .  Full seeker package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

clinUtils  
General Utility Functions for Analysis of Clinical Data
Utility functions to facilitate the import, the reporting and analysis of clinical data. Example ...
Download / Learn more Package Citations See dependency  
ncodeR  
Techniques for Automated Classifiers
A set of techniques that can be used to develop, validate, and implement automated classifiers. A po ...
Download / Learn more Package Citations See dependency  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA