Streamlined analysis of LINCS L1000 data with the slinky package for R.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 09 2019
01 09 2019
Historique:
received:
09
03
2018
revised:
21
09
2018
accepted:
04
01
2019
pubmed:
11
1
2019
medline:
18
6
2020
entrez:
11
1
2019
Statut:
ppublish
Résumé
The L1000 dataset from the NIH LINCS program holds the promise to deconvolute a wide range of biological questions in transcriptional space. However, using this large and decentralized dataset presents its own challenges. The slinky package was created to streamline the process of identifying samples of interest and their corresponding control samples, and loading their associated expression data and metadata. The package can integrate with workflows leveraging the BioConductor collection of tools by encapsulating the L1000 data as a SummarizedExperiment object. Slinky is freely available as an R package at http://bioconductor.org/packages/slinky.
Identifiants
pubmed: 30629124
pii: 5284904
doi: 10.1093/bioinformatics/btz002
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3176-3177Informations de copyright
© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.