J 2015

TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists

SCHIMEK, Michael G., Eva BUDINSKÁ, Karl G. KUGLER, Vendula ŠVENDOVÁ, Jie DING et. al.

Základní údaje

Originální název

TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists

Autoři

SCHIMEK, Michael G. (40 Rakousko), Eva BUDINSKÁ (703 Slovensko, garant, domácí), Karl G. KUGLER (276 Německo), Vendula ŠVENDOVÁ (203 Česká republika), Jie DING (840 Spojené státy) a Shili LIN (840 Spojené státy)

Vydání

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, BERLIN, WALTER DE GRUYTER GMBH, 2015, 2194-6302

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 1.265

Kód RIV

RIV/00216224:14110/15:00083345

Organizační jednotka

Lékařská fakulta

DOI

UT WoS

000355417300008

Klíčová slova anglicky

62G99; 65K10; 68N01; 65C60; 62F07

Štítky

Příznaky

Mezinárodní význam, Recenzováno
Změněno: 9. 7. 2015 14:21, Soňa Böhmová

Anotace

V originále

High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite different technologies, many experiments share the same goal. For instance, the aims of RNA-seq studies often coincide with those of differential gene expression experiments based on microarrays. As such, it would be logical to utilize all available data. However, there is a lack of biostatistical tools for the integration of results obtained from different technologies. Although diverse technological platforms produce different raw data, one commonality for experiments with the same goal is that all the outcomes can be transformed into a platform-independent data format - rankings - for the same set of items. Here we present the R package TopKLists, which allows for statistical inference on the lengths of informative (top-k) partial lists, for stochastic aggregation of full or partial lists, and for graphical exploration of the input and consolidated output. A graphical user interface has also been implemented for providing access to the underlying algorithms. To illustrate the applicability and usefulness of the package, we integrated microRNA data of non-small cell lung cancer across different measurement techniques and draw conclusions. The package can be obtained from CRAN under a LGPL-3 license.