ORdensity
"ORdensity" is an R package to identify differentially expressed genes, a crucial task in genomic studies facilitated by microarray technology. This technology captures the expression levels of numerous genes, aiming to pinpoint a select few that show significant differences in expression under various conditions, thus providing insights into disease mechanisms or biological processes.
Developed in 2018 based on a methodology by Irigoien and Arenas, ORdensity stands out for its ability to handle the growing volume of data produced by modern biomedical research through efficient data analysis processes. One of the key advantages of ORdensity is its implementation of parallel computing, which significantly enhances run-time performance when used on standard computers with parallel processing capabilities. This approach, however, might also increase memory usage, which users should consider based on their system's resources.
Topic
Gene expression;Statistics and probability;Microarray experiment;Pathology;RNA-Seq
Detail
Operation: Differential gene expression analysis;Expression profile clustering;Standardisation and normalisation
Software interface: Library
Language: R
License: GNU General Public License >= version 2
Cost: Free with restrictions
Version name: 0.1.0
Credit: Spanish Ministerio de Economia y Competitividad, Basque Government Research Team Grant, University of the Basque Country UPV/EHU, Spanish Ministerio de Economia y Competitividad, Departament d’Economia i Coneixement de la Generalitat de Catalunya.
Input: -
Output: -
Contact: Concepción Arenas carenas@ub.edu
Collection: -
Maturity: -
Publications
- ORdensity: user-friendly R package to identify differentially expressed genes.
- Martínez-Otzeta JM, et al. ORdensity: user-friendly R package to identify differentially expressed genes. ORdensity: user-friendly R package to identify differentially expressed genes. 2020; 21:135. doi: 10.1186/s12859-020-3463-4
- https://doi.org/10.1186/S12859-020-3463-4
- PMID: 32264950
- PMC: PMC7137194
Download and documentation
Documentation: https://github.com/rsait/ORdensity/blob/master/README.md
Home page: https://github.com/rsait/ORdensity
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