ARSER statistics
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
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.
ARSER in publications
(17)Genome wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns
[…] 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 […]
Modeling Individual Cyclic Variation in Human Behavior
[…] 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 […]
[…] 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 […]
Temporal Control of Metabolic Amplitude by Nocturnin
[…] 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 […]
Transcriptomic analyses reveal rhythmic and CLOCK driven pathways in human skeletal muscle
[…] 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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