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ARSER specifications

Information


Unique identifier OMICS_13327
Name ARSER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Microarray data file with a header line which records the time-points. The 1st column is probesets, other columns are expression values over time. It is assumed that the samples are linearly spaced (e.g., one point every 4 hrs, etc).
Output data Analytical results
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Scipy, Numpy, Matplotlib, Rpy2
Maintained Yes

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Maintainer


  • person_outline Zhen Su <>

Publication for ARSER

ARSER in publications

 (17)
PMCID: 5904149
PMID: 29666379
DOI: 10.1038/s41467-018-03922-5

[…] plot and the histogram of the phase value differences., the oscillation queries of the genomic bins and genes were performed using metacycle software with the rhythmic signal detection methods ars (arser), jtk (jtk_cycle) and ls (lomb-scargle). for genomic bins, we used jtk and ls methods and applied 0.05 p-value cutoff. for genic ts and nts oscillation detection, we applied the three methods […]

PMCID: 5959299
DOI: 10.1145/3178876.3186052

[…] from all three major areas of related work: classical techniques (fourier transform and autocorrelation), data-mining techniques (partial periodicity detection) and circadian rhythm detection (the arser algorithm): discrete fourier transform []: for each feature, we perform a discrete fourier transform and take the period of the peak with the largest amplitude. we take the median […]

PMCID: 5813328
PMID: 29444635
DOI: 10.1186/s12870-018-1244-2

[…] e determination of existence of a circadian biological rhythm represented in the transcriptome data [] using the r package “metacycle” that provides functions and methods (jtk_cycle, lomb-scargle and arser) for detecting rhythmic signals from time series datasets (https://cran.r-project.org/web/packages/metacycle/index.html). jtk_cycle results include the p value (pval, significative if p < 0.0 […]

PMCID: 5815321
PMID: 29386110
DOI: 10.1016/j.celrep.2018.01.011

[…] diurnal rhythmicity, similar to previous reports that examined circadian gene expression in wt mice (). predictively, more stringent q values reduced the number of cycling genes with both the arser (ars) and the jonckheere-terpstra-kendall (jtk) algorithms (; ). however, although similar in number, only about half the cycling transcripts from each genotype were identified in both wt […]

PMCID: 5902165
PMID: 29658882
DOI: 10.7554/eLife.34114.037

[…] order to compare their results with established and widely used algorithms that detect rhythmic profiles, such as jtk_cycle (hughes et al., 2010) and meta cycle (wu et al., 2016) that incorporates arser, jtk_cycle and lomb–scargle., 4) it would be interesting to compare the genes identified as rhythmic in cultured u2os cells (krishnaiah et al., 2017) with the ones identified in the current […]


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ARSER institution(s)
Division of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
ARSER funding source(s)
This work was supported by the Ministry of Science and Technology of China (2008AA02Z312, 2006CB100105).

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