About

NormalyzerDE was developed by Jakob Willforss in the Computational Proteomics group, department of Immunotechnology at Lund University.

NormalyzerDE is available through Bioconductor, currently the development branch.
Source code is available at GitHub.

A Singularity container with NormalyzerDE installed together with its dependencies is available at Singularity Hub.

Normalyzer, the predecessor of NormalyzerDE is found here.

Citations

Citing NormalyzerDE:

Willforss, J., Chawade, A., Levander, F. NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis. Journal of Proteome Research 2018, 10.1021/acs.jproteome.8b00523.

Furthermore, NormalyzerDE makes use of a range of software from the R- and BioConductor ecosystem. When used, please cite:

  • R/Bioconductor:
    Gentleman et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5, (10), R80.
  • Quantile normalization (preprocessCore package):
    Bolstad, B., preprocessCore: A collection of pre-processing functions. 2018
  • VSN normalization (vsn package):
    Huber, W.; von Heydebreck, A.; Sultmann, H.; Poustka, A.; Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18 Suppl 1, S96-104
  • LOESS normalization (Limma package):
    Smyth, G. K., Limma: Linear Models for Microarray Data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Gentleman, R.; Carey, V. J.; Huber, W.; Irizarry, R. A.; Dudoit, S., Eds. Springer New York, 2005.
  • Limma differential expression analysis
    Ritchie, M. E.; Phipson, B.; Wu, D.; Hu, Y.; Law, C. W.; Shi, W.; Smyth, G. K. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015, 43, e47.

Disclaimer

Disclaimer "NormalyzerDE" is provided by the Department of Immunotechnology, Lund University (LU). "NormalyzerDE" is provided "as is" and LU and it's employees make no warrany, express or implied, as to the usefulness of the software/service and documentation for any purpose. By using "Normalyzer" you accept that under no cirumstances will LU and it's employees be liable for any kind of damages that may arise from using this software/service.