transcriptogramer-package: Transcriptional analysis based on transcriptograms
In arthurvinx/transcriptogramer: Transcriptional analysis based on transcriptograms
transcriptogramer-package R Documentation
Transcriptional analysis based on transcriptograms
Description
R package for transcriptional analysis based on transcriptograms, a method
to analyze transcriptomes that projects expression values on a set of
ordered proteins, arranged such that the probability that gene products
participate in the same metabolic pathway exponentially decreases with the
increase of the distance between two proteins of the ordering.
Transcriptograms are, hence, genome wide gene expression profiles that
provide a global view for the cellular metabolism, while indicating gene
sets whose expression are altered.
Author(s)
Diego Morais <vinx@ufrn.edu.br> [maintainer]
Rodrigo Dalmolin <rodrigo.dalmolin@imd.ufrn.br>
References
da Silva, S. R. M., Perrone, G. C., Dinis, J. M., and de Almeida, R. M. C. (2014). Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. BMC Genomics.
de Almeida, R. M. C., Clendenon, S. G., Richards, W. G., Boedigheimer, M., Damore, M., Rossetti, S., Harris, P. C., Herbert, B. S., Xu, W. M., Wandinger-Ness, A., Ward, H. H., Glazier, J. A. and Bacallao, R. L. (2016). Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Human Genomics, 10(1), 1–24.
Ferrareze, P. A. G., Streit, R. S. A., Santos, P. R. dos, Santos, F. M. dos, de Almeida, R. M. C., Schrank, A., Kmetzsch, L., Vainstein, M. H. and Staats, C. C. (2017). Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection. Microorganisms.
Morais, D. A. A., Almeida, R. M. C. and Dalmolin, R. J. S. (2019). Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein–protein interaction. Bioinformatics.
Rybarczyk-Filho, J. L., Castro, M. A. A., Dalmolin, R. J. S., Moreira, J. C. F., Brunnet, L. G., and de Almeida, R. M. C. (2011). Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Research, 39(8), 3005-3016.
Xavier, L. A. da C., Bezerra, J. F., de Rezende, A. A., Oliveira, R. A. de C., Dalmolin, R. J. S., do Amaral, V. S. (2017). Analysis of genome instability biomarkers in children with non-syndromic orofacial clefts. Mutagenesis, 32(2), 313–321.
See Also
Github: source code,
bug reports
References: (da Silva et al., 2014;
de Almeida et al., 2016;
Ferrareze et al., 2017;
Morais et al., 2019;
Rybarczyk-Filho et al., 2011;
Xavier et al., 2017)
arthurvinx/transcriptogramer documentation built on March 21, 2023, 9:15 a.m.
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| transcriptogramer-package | R Documentation |
Transcriptional analysis based on transcriptograms
Description
R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expression are altered.
Author(s)
Diego Morais <vinx@ufrn.edu.br> [maintainer]
Rodrigo Dalmolin <rodrigo.dalmolin@imd.ufrn.br>
References
da Silva, S. R. M., Perrone, G. C., Dinis, J. M., and de Almeida, R. M. C. (2014). Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. BMC Genomics.
de Almeida, R. M. C., Clendenon, S. G., Richards, W. G., Boedigheimer, M., Damore, M., Rossetti, S., Harris, P. C., Herbert, B. S., Xu, W. M., Wandinger-Ness, A., Ward, H. H., Glazier, J. A. and Bacallao, R. L. (2016). Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Human Genomics, 10(1), 1–24.
Ferrareze, P. A. G., Streit, R. S. A., Santos, P. R. dos, Santos, F. M. dos, de Almeida, R. M. C., Schrank, A., Kmetzsch, L., Vainstein, M. H. and Staats, C. C. (2017). Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection. Microorganisms.
Morais, D. A. A., Almeida, R. M. C. and Dalmolin, R. J. S. (2019). Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein–protein interaction. Bioinformatics.
Rybarczyk-Filho, J. L., Castro, M. A. A., Dalmolin, R. J. S., Moreira, J. C. F., Brunnet, L. G., and de Almeida, R. M. C. (2011). Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucleic Acids Research, 39(8), 3005-3016.
Xavier, L. A. da C., Bezerra, J. F., de Rezende, A. A., Oliveira, R. A. de C., Dalmolin, R. J. S., do Amaral, V. S. (2017). Analysis of genome instability biomarkers in children with non-syndromic orofacial clefts. Mutagenesis, 32(2), 313–321.
See Also
Github: source code, bug reports
References: (da Silva et al., 2014; de Almeida et al., 2016; Ferrareze et al., 2017; Morais et al., 2019; Rybarczyk-Filho et al., 2011; Xavier et al., 2017)
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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