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seeker
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]
[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:
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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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