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

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.

Basic information

Original name

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

Authors

SCHIMEK, Michael G. (40 Austria); Eva BUDINSKÁ (703 Slovakia, guarantor, belonging to the institution); Karl G. KUGLER (276 Germany); Vendula ŠVENDOVÁ (203 Czech Republic); Jie DING (840 United States of America) and Shili LIN (840 United States of America)

Edition

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

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10600 1.6 Biological sciences

Country of publisher

Germany

Confidentiality degree

is not subject to a state or trade secret

Impact factor

Impact factor: 1.265

RIV identification code

RIV/00216224:14110/15:00083345

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1515/sagmb-2014-0093

UT WoS

000355417300008

EID Scopus

2-s2.0-84930725526

Keywords in English

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

Abstract

In the original language

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.

Cite

SCHIMEK, Michael G.; Eva BUDINSKÁ; Karl G. KUGLER; Vendula ŠVENDOVÁ; Jie DING and Shili LIN. TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY. BERLIN: WALTER DE GRUYTER GMBH, 2015, vol. 14, No 3, p. 311-316. ISSN 2194-6302. Available from: https://dx.doi.org/10.1515/sagmb-2014-0093.

@article{1305886,
   author = {Schimek, Michael G. and Budinská, Eva and Kugler, Karl G. and Švendová, Vendula and Ding, Jie and Lin, Shili},
   article_location = {BERLIN},
   article_number = {3},
   doi = {http://dx.doi.org/10.1515/sagmb-2014-0093},
   keywords = {62G99; 65K10; 68N01; 65C60; 62F07},
   language = {eng},
   issn = {2194-6302},
   journal = {STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY},
   title = {TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists},
   volume = {14},
   year = {2015}
}

TY  - JOUR
ID  - 1305886
AU  - Schimek, Michael G. - Budinská, Eva - Kugler, Karl G. - Švendová, Vendula - Ding, Jie - Lin, Shili
PY  - 2015
TI  - TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
JF  - STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY
VL  - 14
IS  - 3
SP  - 311-316
EP  - 311-316
PB  - WALTER DE GRUYTER GMBH
SN  - 21946302
KW  - 62G99
KW  - 65K10
KW  - 68N01
KW  - 65C60
KW  - 62F07
N2  - 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.
ER  -

SCHIMEK, Michael G.; Eva BUDINSKÁ; Karl G. KUGLER; Vendula ŠVENDOVÁ; Jie DING and Shili LIN. TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. \textit{STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY}. BERLIN: WALTER DE GRUYTER GMBH, 2015, vol.~14, No~3, p.~311-316. ISSN~2194-6302. Available from: https://dx.doi.org/10.1515/sagmb-2014-0093.

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