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", "1.1.5")



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 1.1.5, https://cran.r-project.org/web/packages/seeker
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)
Other packages that cited seeker R package
View seeker citation profile
Other R packages that seeker depends, imports, suggests or enhances
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

gclus  
Clustering Graphics
Orders panels in scatterplot matrices and parallel coordinate displays by some merit index. Package ...
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  
CompoundEvents  
Statistical Modeling of Compound Events
Tools for extracting occurrences, assessing potential driving factors, predicting occurrences, and q ...
Download / Learn more Package Citations See dependency  
MatrixEQTL  
Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for associat ...
Download / Learn more Package Citations See dependency  
ismev  
An Introduction to Statistical Modeling of Extreme Values
Functions to support the computations carried out in `An Introduction to Statistical Modeling of Ex ...
Download / Learn more Package Citations See dependency  
stagePop  
Modelling the Population Dynamics of a Stage-Structured Species in Continuous Time
Provides facilities to implement and run population models of stage-structured species... ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns