slinky

DOI: 10.18129/B9.bioc.slinky    

This is the development version of slinky; to use it, please install the devel version of Bioconductor.

Putting the fun in LINCS L1000 data analysis

Bioconductor version: Development (3.10)

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 J. Kort

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

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.1
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
License MIT + file LICENSE
Depends R (>= 3.5.0)
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_1.3.1.tar.gz
Windows Binary slinky_1.3.1.zip
Mac OS X 10.11 (El Capitan) slinky_1.3.1.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: