DanteR protocols

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DanteR specifications

Information


Unique identifier OMICS_02489
Name DanteR
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Richard Smith <>

Publication for DanteR

DanteR in pipelines

 (2)
2016
PMCID: 4992866
PMID: 27545962
DOI: 10.1038/srep31697

[…] added. search results were filtered and only high confidence peptides with xcorr 2.0 or more were used for further analysis. relative quantification was done with protmax 2012 tool version 2.14 and danter software. for that, the thermo raw files were converted to mzxml format with massmatrix mm file conversion tool and quantification was done in protmax by summing parent ion intensities. […]

2016
PMCID: 5342125
PMID: 27708245
DOI: 10.18632/oncotarget.12376

[…] on the log2-values of the measured peptide intensities and the data were normalised based on the median. modified peptides were merged with the r rollup function (http://omics.pnl.gov/software/danter) allowing for one-hit-wonders and using the mean of the normalised intensities for each peptide. quantification of proteins was obtained by merging the unmodified peptides with the r rollup […]


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DanteR in publications

 (31)
PMCID: 5855760
PMID: 29439444
DOI: 10.3390/ijms19020538

[…] 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 permissions and/or licenses for the study has been achieved., […]

PMCID: 5823648
PMID: 29507698
DOI: 10.18632/oncotarget.24321

[…] identifier pxd005245., peptides abundancies reported by proteome discoverer were log2 transformed, normalized by subtracting the mean, and protein rollup was performed using rrollup method from danter package []. log2-transformed intensities were used for hierarchical clustering and cv calculation prior to normalization. significantly regulated proteins were detected using limma r package […]

PMCID: 5741201
PMID: 28844130
DOI: 10.15283/ijsc17036

[…] fdr (false discovery rate) analysis was selected. a minimum of five peptide cut-off stringency was used to identify proteins. volcano plots, gene ontology and bioplex heat maps were generated using danter software ()., human adscs (hadscs) were cultured producing a morphologically homogenous culture with cells exhibiting the spindle-fibroblastic form consistent with current literature. […]

PMCID: 5598967
PMID: 28910307
DOI: 10.1371/journal.pone.0184259

[…] and the landscape setting was explored., this study was not carried out in national parks or other protected areas of land or sea or on private land. sampling was conducted under the auspice of danter cachique huansi (co-author) from the peruvian amazon research institute (pari), tarapoto, peru as a responsible person for plukenetia volubilis cultivation and breeding in pari., specific […]

PMCID: 5409181
PMID: 28453527
DOI: 10.1371/journal.pone.0176462

[…] peptides that were not identified in either the nuclear or cytoplasmic fraction were excluded. peptide abundances were then “rolled up” to the protein level using the r-rollup method implemented in danter [] (). peptides that were mapped to multiple proteins were included in the normalization procedure but excluded from the protein quantification step., three sets of nsc34 cells (transfected […]


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DanteR institution(s)
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

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