Bioclipse-R: integrating management and visualization of life science data with statistical analysis

O. Spjuth; V. Georgiev; L. Carlsson; J. Alvarsson; A. Berg; E. Willighagen; J. E. Wikberg; M. Eklund

doi:10.1093/bioinformatics/bts681

Bioclipse-R: integrating management and visualization of life science data with statistical analysis

O. Spjuth, V. Georgiev, L. Carlsson, J. Alvarsson, A. Berg, E. Willighagen, J. E. Wikberg, M. Eklund^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

SUMMARY: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system. Availability and implementation: Bioclipse-R is implemented as a set of Java plug-ins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: martin.eklund@farmbio.uu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	286-289
Journal	Bioinformatics
Volume	29
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/bts681
Publication status	Published - 1 Jan 2013

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10.1093/bioinformatics/bts681Licence: CC BY

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Cite this

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title = "Bioclipse-R: integrating management and visualization of life science data with statistical analysis",

abstract = "SUMMARY: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system. Availability and implementation: Bioclipse-R is implemented as a set of Java plug-ins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: martin.eklund@farmbio.uu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "O. Spjuth and V. Georgiev and L. Carlsson and J. Alvarsson and A. Berg and E. Willighagen and Wikberg, {J. E.} and M. Eklund",

year = "2013",

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doi = "10.1093/bioinformatics/bts681",

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T1 - Bioclipse-R: integrating management and visualization of life science data with statistical analysis

AU - Spjuth, O.

AU - Georgiev, V.

AU - Carlsson, L.

AU - Alvarsson, J.

AU - Berg, A.

AU - Willighagen, E.

AU - Wikberg, J. E.

AU - Eklund, M.

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N2 - SUMMARY: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system. Availability and implementation: Bioclipse-R is implemented as a set of Java plug-ins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: martin.eklund@farmbio.uu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system. Availability and implementation: Bioclipse-R is implemented as a set of Java plug-ins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: martin.eklund@farmbio.uu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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