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TWILIGHT specifications

Information


Unique identifier OMICS_14939
Name TWILIGHT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.56.0
Stability Stable
Requirements
stats, graphics, Biobase, grDevices, R(>=2.10), Biobase(>=1.12.0), splines(>=2.2.0), stats(>=2.2.0), golubEsets(>=1.4.2), vsn(>=1.7.2)
Maintained Yes

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Documentation


Maintainer


  • person_outline Volker Brendel

Publication for TWILIGHT

TWILIGHT citations

 (4)
library_books

Network Modeling Identifies Molecular Functions Targeted by miR 204 to Suppress Head and Neck Tumor Metastasis

2010
PLoS Comput Biol
PMCID: 2848541
PMID: 20369013
DOI: 10.1371/journal.pcbi.1000730

[…] on in both GSE6631 and GSE2379 (data not shown). An empirical Student T-test for unequal variances was performed to compare Δ for each microRNA between cancer and normal tissue (Bioconductor package twilight, 1,000 permutation resampling, “paired t-test”for GSE6631, “unpaired t-test” for GSE2379 ). To adjust for multiple comparisons (different microRNAs on the same dataset), we calculate a Benjam […]

library_books

From protein interactions to functional annotation: graph alignment in Herpes

2008
BMC Syst Biol
PMCID: 2607256
PMID: 18957106
DOI: 10.1186/1752-0509-2-90

[…] roteins have an amino acid sequence identity of only about 20%. Moreover, many open reading frames are only about 60 amino acids long. Thus, the sequence similarity between the two species is in the 'twilight zone' of detection by alignment, i.e., orthologous open reading frames have alignment scores just marginally above the background of unrelated sequences.To improve the cross-species compariso […]

library_books

A constrained polynomial regression procedure for estimating the local False Discovery Rate

2007
BMC Bioinformatics
PMCID: 1940264
PMID: 17603882
DOI: 10.1186/1471-2105-8-229

[…] t's statistic. Then, we estimated lFDR from our procedure, referred to as polfdr, and the four procedures presented in the background section, referred to as locfdr (Efron), LocalFDR (Aubert et al.), twilight (Scheid and Spang), pava.fdr (Broberg). Although these procedures were not designed to estimate the probability π0 independently of lFDR, we also compared the estimators of π0 obtained from t […]

library_books

A comparative review of estimates of the proportion unchanged genes and the false discovery rate

2005
BMC Bioinformatics
PMCID: 1199583
PMID: 16086831
DOI: 10.1186/1471-2105-6-199

[…] e tuning parameter λ.A local FDR is obtained from smoothed histogram estimates based on equidistant bins,where the function h0 refers to the Jfinal set and h to the total set of p-values.The function twilight in package twilight provides an implementation of SEP []. […]


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TWILIGHT institution(s)
Max Planck Institute for Molecular Genetics, Computational Diagnostics, Berlin, Germany
TWILIGHT funding source(s)
This work was supported by BMBF grants 031U109C and 03U117.

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