GeneCycle protocols

View GeneCycle computational protocol

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GeneCycle specifications

Information


Unique identifier OMICS_13332
Name GeneCycle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.2
Stability Stable
Requirements
MASS, R(≥2.7.0), longitudinal(≥1.1.3), fdrtool(≥ 1.2.5)
Maintained Yes

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Maintainer


  • person_outline Miika Ahdesmaki <>

Publications for GeneCycle

GeneCycle in pipelines

 (2)
2014
PMCID: 4245765
PMID: 25403374
DOI: 10.1186/s12870-014-0308-1

[…] expressed targets that showed statistically significant differences in expression (false discovery rate q-value ≤0.05) in the normalized datasets of 36 summer samples were identified using the genecycle r package []. subsequently, we compared all possible combinations of average expression value at each time point, and selected expressed targets with more than two-fold differences […]

2009
PMCID: 2758837
PMID: 19758441
DOI: 10.1186/1752-0509-3-93

[…] entry in cyclebase.org []. the periodicity and dominant fourier frequency for the log10(tfa) profiles were determined with fisher's g-statistic (table ) and the average periodogram (figure ) using genecycle []. the module network (additional file ) was computed using four cdc25 and four elu data (oliva elu 1&2 not used) with genomica []. gene ontology based associations were computed […]


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GeneCycle in publications

 (11)
PMCID: 5532269
PMID: 28751729
DOI: 10.1038/s41598-017-06110-5

[…] and cytoscape (v3.1.0), location of related clusters was visualized by circos. gene expression periodicity was measured on 120 interpolated expression values for each replicate time series using genecycle, candidate periodically expressed genes were identified as having the same calculated dominant cycling frequency between biological replicates. time-dependent expression signatures […]

PMCID: 5383398
PMID: 28384097
DOI: 10.7554/eLife.24695.029

[…] prerequisite for this analysis. the distance spectrum of rpfs from mrnas already showed a 3-nt periodicity pattern. we then transformed the distance spectrum using the ‘periodogram’ function of the genecycle package () with the ‘clone’ method. the relative spectral density was calculated by normalizing to the value at the third position., we used the same dynamic programming algorithm […]

PMCID: 4709092
PMID: 26751389
DOI: 10.1371/journal.pone.0146643

[…] was separated and analyzed for periods of 24 hours (circwave and periods between 19 and 28 hours (circwave batch, p<0.02). periodogram analysis was performed using r statistical program and the genecycle package [] followed by fisher's exact g test to obtain p-values of each culture. spread/motility measures, periods, amplitudes, and damping coefficients were compared by 1- or 2-way anova, […]

PMCID: 4666670
PMID: 26624004
DOI: 10.1371/journal.pone.0143412

[…] numbers; dra003530, dra003529 and dra003528). histogram analyses with rpkm values of <0.1 were set to 0.1, and rpkm values were log (2) transformed. statistical analyses were performed using the genecycle and samr packages of r software. p-values were calculated using fisher’s exact g test, and sorting data for heatmaps were as follows: 24-h cycle; maximum value, 7 (time, 6:00); minimum […]

PMCID: 4556673
PMID: 26325287
DOI: 10.1371/journal.pone.0136851

[…] false discovery rate (fdr) [–]. fdr <0.2 was considered significant []. to compare protein expression levels across multiple generations, a g-statistic was used []. r packages including genecycle, q value and classcomparison were employed []., forty-eight viable tumors were implanted from 47 patients: one patient had a bilateral tumor implanted as separate models. implants […]


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GeneCycle institution(s)
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland; Institute for Systems Biology, WA, USA; Marine Environmental Biology, University of Southern California, CA, USA; ProSanos Corporation, Harrisburg, PA, USA; Department of Statistics, University of Munich, Munich, Germany; Department of Mathematics and Statistics, University of Cyprus, Nicosia, Cyprus
GeneCycle funding source(s)
This work was supported by an Emmy Noether research grant (STR 624/1-2) from the Deutsche Forschungsgemeinschaft, Tampere Graduate School in Information Science and Engineering and the Academy of Finland, project No. 213462 (Finnish Centre of Excellence program (2006 – 2011)), and R01 GM072855 grant from NIH.

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