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("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 | ||
| 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 | |
| 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 |