Cyber-T protocols

View Cyber-T computational protocol

Cyber-T statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differential expression Normalization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Cyber-T specifications

Information


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

Documentation


Maintainer


  • person_outline Pierre Baldi <>

Additional information


A registration is needed to access to tools.

Information


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
Requirements
Lattice, vsn, multtest, geneplotter
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Pierre Baldi <>

Additional information


A registration is needed to access to tools.

Publications for Cyber-T

Cyber-T in pipelines

 (4)
2015
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. […]

2013
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 […]

2011
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, […]

2011
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 […]


To access a full list of citations, you will need to upgrade to our premium service.

Cyber-T in publications

 (133)
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 (www.bioconductor.org). 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

Cyber-T reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Cyber-T