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propr specifications


Unique identifier OMICS_15518
Name propr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 4.0.0
Stability Stable
limma, methods, stats, grid, Biobase, utils, testthat, grDevices, Rcpp, ggplot2, data.table, rmarkdown, knitr, reshape2, igraph, rgl, ggdendro, datasets, R(≥3.2.2), fastcluster, plotly, ALDEx2, cccrm, compositions, SDMTools
Maintained Yes


No version available



  • person_outline Thomas Quinn

Publication for propr

propr citations


propr: An R package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

Sci Rep
PMCID: 5701231
PMID: 29176663
DOI: 10.1038/s41598-017-16520-0

[…] cks a scale that would otherwise make it possible to compare dependency across multiple feature pairs. In essence, what we call proportionality is a modification to the VLR that establishes scale.The propr package, now available through the Comprehensive R Archive Network (CRAN), implements two measures of proportionality, ϕ and ρ p (defined formally in the next section). Like the Pearson correl […]


Microbiome Datasets Are Compositional: And This Is Not Optional

Front Microbiol
PMCID: 5695134
PMID: 29187837
DOI: 10.3389/fmicb.2017.02224

[…] rix, and the ϕ (Lovell et al., ) and ρ (Erb and Notredame, ) metrics (the published versions of which required a non-sparse matrix). These latter two metrics have been incorporated into the R package propr, that includes an adaptation allowing the calculation of the metrics with sparse data that gives an expected value of ρ (E(ρ)), that approaches 1 if the two features have exactly constant ratios […]


Identification and analysis of MKK and MPK gene families in canola (Brassica napus L.)

BMC Genomics
PMCID: 3701561
PMID: 23758924
DOI: 10.1186/1471-2164-14-392

[…] s also requires the participation of the AtMKK1 and AtMPK3 and -6 []. AtMKK3 could act upstream of group C MPKs (MPK1, -2, -7 and -14) to regulate the downstream pathogenesis-related (PR) genes since ProPR1::GUS expression was enhanced by the co-expression of AtMKK3/AtMPK7. AtMKK3-overexpression lines with increased PR gene expression are tolerant while the knock-out mkk3 lines are susceptible to […]

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propr institution(s)
Bioinformatics Core Research Group, Deakin University, Geelong, VIC, Australia; School of Medicine, MMR, Deakin University, Geelong, VIC, Australia; Queensland University of Technology, Brisbane, QLD, Australia

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