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: 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 24 Apr. 2025.
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), 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
03/2803/3004/0104/0204/0504/0604/0704/0804/0904/1204/1304/1504/1704/1804/1904/2104/22Downloads for seeker024681012141618202224TrendBars

Today's Hot Picks in Authors and Packages

clustMixType  
k-Prototypes Clustering for Mixed Variable-Type Data
Functions to perform k-prototypes partitioning clustering for mixed variable-type data according to ...
Download / Learn more Package Citations See dependency  
PQLseq  
Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Sequencing Studies
An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and ...
Download / Learn more Package Citations See dependency  
stratbr  
Optimal Stratification in Stratified Sampling
An Optimization Algorithm Applied to Stratification Problem.This function aims at constructing optim ...
Download / Learn more Package Citations See dependency  
rattle  
Graphical User Interface for Data Science in R
The R Analytic Tool To Learn Easily (Rattle) provides a collection of utilities functions for the d ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
TeachHist  
A Collection of Amended Histograms Designed for Teaching Statistics
Statistics students often have problems understanding the relation between a random variable's true ...
Download / Learn more Package Citations See dependency  

24,098

R Packages

207,311

Dependencies

65,069

Author Associations

24,099

Publication Badges

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