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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: 2023-05-23
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 07 Nov. 2024.
Previous versions and publish date:
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)
Other packages that cited seeker R package
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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
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