biRte protocols

View biRte computational protocol

biRte statistics

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Associated diseases

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biRte specifications

Information


Unique identifier OMICS_09223
Name biRte
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 1.16.0
Stability Stable
Requirements
stats, graphics, Biobase, utils, Rcpp, knitr, MASS, R(>=3.0.0), nem, glmnet, RcppArmadillo(>=0.3.6.1), limma(>=3.22.0)
Maintained Yes

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Documentation


Maintainer


  • person_outline Holger Fröhlich <>

Publications for biRte

biRte in pipeline

2017
PMCID: 5369021
PMID: 28347313
DOI: 10.1186/s12918-017-0419-z

[…] network with 344 tfs is compiled by computing tf binding affinities to promoter sequences according to the trap model [] using data from ensembl, transfac, jaspar and metacore™. an implementation of birte is available for r on bioconductor under https://bioconductor.org/packages/release/bioc/html/birte.html., several simulations were conducted to study model behavior. on the basis of a human […]


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biRte in publications

 (112)
PMCID: 5934831
PMID: 29724207
DOI: 10.1186/s12913-018-3141-7

[…] and employees in the cancer departments in both case hospitals for taking their time to share important knowledge and their experience with us. we would also like to acknowledge the coordinator birte fagerdal for generously organizing the data collection for this study. we would also like to thank the reviewers for their valuable comments and input to improve the article., stavanger […]

PMCID: 5929412
PMID: 29731969
DOI: 10.18632/oncotarget.24701

[…] the chi- square as well as the mann-whitney-u-test was used when appropriate. all statistical investigations were conducted using graphpad prism 6 and spss 24 (ibm)., the authors would like to thank birte mergelkuhl and rudina marx for their dedicated administrative assistance., conflicts of interest , the authors declare no conflicts of interest., author contributions , study concept: ng, hw. […]

library_books

Author Index

PMCID: 5888218
DOI: 10.1093/schbul/sby048

[…] anthony, s39, gizdic, alena, s196, gjestad, rolf, s324, s346, s358, gladyshev, igor, s213, glass, steven, s236, s341, glatard, anaïs, s310, glausier, jill , s29, gleeson, john f, s4, glenthøj, birte y., s289, glenthøj, birte, s80, s213, s383, s424, glenthøj, louise birkedal, s119, glenthoj, birte, s50, s83, s119, s224, s226, s232, s314, s387, s422, glerean, enrico, s47, glynn, shirley, […]

PMCID: 5857561
PMID: 29593651
DOI: 10.3389/fendo.2018.00084

[…] this work and, as such, had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. the authors thank gundula hertl, birte hussmann, and doris erb for expert advice and technical assistance. the authors thank prof. dr. lillig, department of medical biochemistry and molecular biology, ernst-moritz arndt-university […]

PMCID: 5826961
PMID: 29520296
DOI: 10.3389/fgene.2018.00049

[…] the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., we are indebted to diana maron, tajana jungbauer, birte rings, verena popp, petra badorf, and verena kollera for their expert technical assistance. this study was funded by the german research foundation dfg (np-dfg_bu 2878/2-1) […]


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biRte institution(s)
University of Bonn, Institute for Computer Science, Bonn-Aachen International Center for IT (B-IT), Bonn, Germany

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