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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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Versioning
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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 citations
(17)Genome wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns
[…] 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 an […]
Diel pattern of circadian clock and storage protein gene expression in leaves and during seed filling in cowpea (Vigna unguiculata)
[…] 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 < 0.05), […]
Temporal Control of Metabolic Amplitude by Nocturnin
[…] ificant 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 and KO […]
Episode like pulse testosterone supplementation induces tumor senescence and growth arrest down modulating androgen receptor through modulation of p ERK1/2, pARser81 and CDK1 signaling: biological implications for men treated with testosterone replacement therapy
[…] n extracts from LNCaP and CW22Rv1 treated with pulsed or continuous T concentrations. We found that both LNCaP and CW22rv1 cells exposed to pulsed T treatment (Figure ) showed a marked reduction of p-ARser81 levels, while only continuous treatment with high T (17.2 nM) concentration was able to reduce p-ARser81 levels in CW22rv1 cells. Accordingly, when we evaluated the levels of cyclin-dependent […]
Guidelines for Genome Scale Analysis of Biological Rhythms
[…] re are numerous high-quality statistical approaches for detecting rhythmicity and estimating rhythmic parameters in large data sets. These include but are not limited to Haystack (), Lomb-Scargle (), ARSER (), CircWaveBatch (), JTK_Cycle (), and its successors, RAIN (), eJTK (), and ABSR (). Each has different strengths and weaknesses. To briefly summarize these methods, tests based on curve fitti […]
Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum
[…] Sequencing outputs and bioinformatics treatments were carefully analyzed and checked several times to ensure the reliability of data supporting the discussion. Cycling transcripts were detected using ARSER with MetaCycle (version 1.1.0 on R (32-bit, version 3.2.2)). ARSER algorithm was developed and applied to high-throughput time-series analysis and particularly adapted to experimental designs wi […]
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