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

DOI: 10.18129/B9.bioc.slinky

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>

Citation (from within R, enter citation("slinky")):

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")

LINCS analysis with slinky HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DifferentialExpression, GeneExpression, GeneSetEnrichment, PatternLogic, Software, ThirdPartyClient

Version 1.12.0

In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)

License MIT + file LICENSE

Depends R (>= 4.1)

Imports SummarizedExperiment, curl, dplyr, foreach, httr, stats, utils, methods, readr, rhdf5, jsonlite, tidyr

System Requirements

URL

Suggests GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report 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

Old Source Packages for BioC 3.14 Source Archive