Cyber-T protocols

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Cyber-T statistics

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Cyber-T specifications


Unique identifier OMICS_15281
Name Cyber-T
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Python, R
Database management system PostgreSQL
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Pierre Baldi <>

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Unique identifier OMICS_15281
Name Cyber-T
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Lattice, vsn, multtest, geneplotter
Maintained Yes



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  • person_outline Pierre Baldi <>

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Publications for Cyber-T

Cyber-T in pipelines

PMCID: 4391502
PMID: 25647729
DOI: 10.7554/eLife.04525.019

[…] arm. significance testing for this alternative analysis of the in vivo mtn-007 data was performed via a linear fit model using the limma package (), with the same significance criteria used for cyber-t. the resulting gene lists greatly overlapped with the cyber-t results. for simplicity, the numbers of induced and suppressed genes reported in ‘results’ are based on the cyber-t analysis. […]

PMCID: 3559497
PMID: 23383279
DOI: 10.1371/journal.pone.0055769

[…] of the probes showing atleast 30% change in expression across the 3 donors were computed and ratios (treatment/control) were log2 transformed. statistical analysis of the data was performed using cyber-t regularized t-statistic due to small sample size (n = 3) since it takes into account bayesian estimate of variance by pooling across genes with similar intensities . differentially regulated […]

PMCID: 3030562
PMID: 21297973
DOI: 10.1371/journal.pone.0016330

[…] to the total number of sequence-reads of the corresponding sample. significant changes of histone acetylation between pair-wise comparisons of different conditions were identified with the cyber-t-test r-module by using all biological replicates and graphically displayed in kernel density estimation plots. significance thresholds were set at p<0.05 for the most variable regions, […]

PMCID: 3231920
PMID: 21995554
DOI: 10.1186/1475-2859-10-S1-S13

[…] converted to data files with feature extraction software (aglient, version 9.1). outliers were identified and removed using the grubbs test [] and the mean of replicate probes was calculated. the cyber-t test [] was employed to calculate p-values. significance was apportioned to genes with an expression ratio ≥5 and a p-value of ≤1.0x10-4. final expression ratios presented are the average […]

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Cyber-T in publications

PMCID: 5829577
PMID: 29294107
DOI: 10.1093/nar/gkx1289

[…] to data files with agilent feature extraction software (version 9.5). dna microarray data sets were processed as previously described (). differential signal intensity tests were performed with the cyber-t implementation of a variant of the t-test (). data were analysed and visualized using the multi-experiment viewer tmev v.4.9 with hierarchical clustering analysis based on covariance method […]

PMCID: 5717538
PMID: 29249983
DOI: 10.3389/fphys.2017.00980

[…] expression values of 12,789 genes across 20 diseases., r (v 3.2.2) (r core team, )/bioconductor (gentleman et al., ) was used for all data processing and pipelines implemented in this analysis., cyber-t's (kayala and baldi, ) regularized t-test performed on z-transformed expression values was used as a measure of a gene's differential activity. the associated t-statistic provided insight […]

PMCID: 5699109
PMID: 29162049
DOI: 10.1186/s12864-017-4299-9

[…] of reads mapped to a gene × 106) / (total mapped input reads in the sample x gene length in kbp). statistical analysis of the rpkm-values between the experimental conditions was performed using cyber-t []. genes were determined to be significantly contributing to growth in human serum when the benjamini-hochberg corrected p-value was <0.05 and the difference in abundance […]

PMCID: 5681666
PMID: 29127379
DOI: 10.1038/s41598-017-15704-y

[…] open-source bioconductor software ( genes differentially expressed between the control and 131r10 or combination with irinotecan groups were identified with bayesian t-test (cyber-t), which combines student’s t-test with a bayesian estimate of the intra-group variance obtained from the observed variance of probe sets at a similar expression levels. for experiments […]

PMCID: 5449479
PMID: 28620359
DOI: 10.3389/fmicb.2017.00964

[…] extraction software (v9.5). the dna microarray data were processed as previously described (garcía de la nava et al., ; van hijum et al., , ). differential expression tests were performed with the cyber-t implementation of a variant of the t-test (long et al., ). a gene was considered to exhibit a significantly different expression level relative to the control when p < 0.001 […]

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Cyber-T institution(s)
Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA
Cyber-T funding source(s)
National Institutes of Health (NIH) (LM010235-01A1 and 5T15LM007743).

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