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InfernoRDN specifications

Information


Unique identifier OMICS_18443
Name InfernoRDN
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 1.1.6109
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Matthew Monroe

Additional information


InfernoRDN is an updated version of Inferno (which used StatconnDCOM). InfernoRDN supersedes all previous DAnTE (Data Analysis Tool Extension), DanteR, and Inferno versions.

InfernoRDN citations

 (11)
library_books

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

2018
MBio
PMCID: 5850319
PMID: 29535201
DOI: 10.1128/mBio.02061-17

[…] by summing together the intensities of all identified peptides and normalized by their respective protein lengths. protein abundances were log2 transformed and median centered across all samples in infernordn version 1.1 ()., to investigate enriched secreted proteins, we performed student’s t tests between the cell pellet and the spent medium (supernatant) samples using the perseus software […]

library_books

Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves

2018
PLoS One
PMCID: 5813909
PMID: 29447168
DOI: 10.1371/journal.pone.0190019

[…] of 10 ppm; no retention time alignment. protein abundances were calculated by summing together their respective peptide intensities. log 2-transformed protein intensities were loaded into the infernordn v1.1 [] software and values were normalized by median centering adjustments across the global dataset., for this study, we performed pair-wise comparisons between the well-watered controls […]

library_books

Multi omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota

2017
mSystems
PMCID: 5655592
PMID: 29085914
DOI: 10.1128/mSystems.00107-17

[…] had a stronger effect on the transcriptome of c57bl/10a mice than on that of balb/c mice, and these effects were largely sex independent (). the ileum transcriptome data were also analyzed using infernordn to discover transcripts affected by sex and/or strain (see fig. s1b in  in the supplemental material) (). the effect of mouse strain on the transcriptome was significant and largely […]

library_books

Enhanced differential expression statistics for data independent acquisition proteomics

2017
Sci Rep
PMCID: 5517573
PMID: 28724900
DOI: 10.1038/s41598-017-05949-y

[…] the peptide-level to improve the accuracy of the results by estimating the significance of median peptide-level p-values using the beta distribution. this approach is different from tools, such as infernordn (formerly known as dante), which roll up already the peptide-level abundances before applying any statistical testing. to demonstrate the benefits of ropeca over the previously published […]

library_books

Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells

2017
Sci Rep
PMCID: 5327387
PMID: 28240279
DOI: 10.1038/srep43583

[…] v. 2.1. peptide spectrum matches were filtered by idpicker v.3 (fdr < 1%), assigned matched-ion intensities, and peptide abundance distributions normalized and assembled to proteins using infernordn, as previously described. for statistical analyses, missing protein abundance values were first imputed with a distribution of values near the limit of detection and one way anova […]

library_books

Genomics informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

2016
Nat Commun
PMCID: 4935971
PMID: 27378076
DOI: 10.1038/ncomms12115

[…] matched-ion intensity. resulting peptide intensity distributions were log2-transformed, normalized across replicates (loess), and standardized by median absolute deviation and median centring using infernordn. protein abundances were derived using the rrollup method as previously described. list the predicted proteins of both organisms and provide a comparison of relative abundance data […]


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