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Normalyzer specifications

Information


Unique identifier OMICS_06720
Name Normalyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Aakash Chawade

Information


Unique identifier OMICS_06720
Name Normalyzer
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Aakash Chawade

Publication for Normalyzer

Normalyzer citations

 (6)
library_books

H2 drives metabolic rearrangements in gas fermenting Clostridium autoethanogenum

2018
Biotechnol Biofuels
PMCID: 5831606
PMID: 29507607
DOI: 10.1186/s13068-018-1052-9

[…] has shown higher quantification accuracy [, ]) and input data were normalised using quantile normalisation, independently determined as the most suitable normalisation method using the software normalyzer []. higher quantification accuracy for the sil proteins was achieved by label-based quantification through normalising light (endogenous) data with heavy (spike-in). proteins […]

library_books

Comparative Membrane Associated Proteomics of Three Different Immune Reactions in Potato

2018
Int J Mol Sci
PMCID: 5855760
PMID: 29439444
DOI: 10.3390/ijms19020538

[…] proteios, and subsequent feature matching and alignment between lc-ms/ms runs with a previously described workflow []. the resulting peptide data was normalized using loess-g normalization [] in the normalyzer software []. the normalized data was analyzed using danter []., all local, national and international guidelines and legislations have been followed and the required or appropriate […]

library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] tools such as mettailor [] that use a dynamic block summarization method for correcting misalignments, reducing missing data, and apply a retention time–based local normalization procedure, or normalyzer [], that uses 12 different well-known normalization methods and compares the results based on different parameters. intcor [] corrects for peak intensity drift effects based on variance […]

library_books

Effects of insulin and the glucagon‐like peptide 1 receptor agonist liraglutide on the kidney proteome in db/db mice

2017
PMCID: 5371560
PMID: 28330952
DOI: 10.14814/phy2.13187

[…] in order to obtain the total peak area for each peptide. srm raw data were normalized with normfinder (andersen et al. ) after evaluation of the optimal normalization method using the software normalyzer 1.1.1 (chawade et al. ). all technical replicates were merged for the statistical analysis., all the proteins included in the confirmatory srm dataset were entered into the protein […]

library_books

N glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models

2016
PMCID: 5065702
PMID: 27757071
DOI: 10.1186/s12014-016-9123-z

[…] is listed in an additional file f. after peptide identification and protein assembly in progenesis, the processed non-normalized data intensities from both mouse models were run through the software normalyzer 1.1.1 [, ]. normalyzer assesses the optimal normalization method for omics data sets compared to log2 transformation and the data sets are validated from both quantitative and qualitative […]

library_books

Stage specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle*

2016
PMCID: 4974336
PMID: 27226403
DOI: 10.1074/mcp.M115.055640

[…] peptide ions and the average abundance of the three top-ranked peptides is used to calculate the protein signal. protein abundance was normalized across samples by average intensity utilizing the normalyzer software package (). dirofilaria immitis excretory-secretory product (esp) spectral data (mgf files obtained from ()) were searched against the d. immitis theoretical proteome […]


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Normalyzer institution(s)
Department of Immunotechnology, Lund University, Lund, Sweden

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