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>

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

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
See More
Suggests GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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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