slinky

DOI: 10.18129/B9.bioc.slinky    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see slinky.

Putting the fun in LINCS L1000 data analysis

Bioconductor version: 3.14

Wrappers to query the L1000 metadata available via the clue.io REST API as well as helpers for dealing with LINCS gctx files, extracting data sets of interest, converting to SummarizedExperiment objects, and some facilities for performing streamlined differential expression analysis of these data sets.

Author: Eric Kort [aut, cre]

Maintainer: Eric Kort <eric.kort at vai.org>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("slinky")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("slinky")

 

HTML	R Script	LINCS analysis with slinky
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, GeneSetEnrichment, PatternLogic, Software, ThirdPartyClient
Version	1.12.0
In Bioconductor since	BioC 3.8 (R-3.5) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	SummarizedExperiment, curl, dplyr, foreach, httr, stats, utils, methods, readr, rhdf5, jsonlite, tidyr
LinkingTo
Suggests	GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	slinky_1.12.0.tar.gz
Windows Binary	slinky_1.12.0.zip
macOS 10.13 (High Sierra)	slinky_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/slinky
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/slinky
Package Short Url	https://bioconductor.org/packages/slinky/
Package Downloads Report	Download Stats