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iOMICS specifications

Information


Unique identifier OMICS_02159
Name iOMICS
Software type Framework/Library
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Parallelization MapReduce
License Commercial
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained No

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iOMICS citations

 (11)
call_split

Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study

2017
Nat Commun
PMCID: 5608948
PMID: 28935855
DOI: 10.1038/s41467-017-00413-x
call_split See protocol

[…] Subjects enrolled in the iOmics were originally recruited for a community-based multi-ethnic prospective cohort that is part of the SPHS project (formerly Singapore Consortium of Cohort Studies), where 122 Chinese, 120 Malays […]

library_books

Comprehensive analysis of human protein N termini enables assessment of various protein forms

2017
Sci Rep
PMCID: 5529458
PMID: 28747677
DOI: 10.1038/s41598-017-06314-9

[…] Sequence logos were made using iceLogo (http://iomics.ugent.be/icelogoserver/index.html) and Weblogo (http://weblogo.berkeley.edu/logo.cgi). All logo images were made with the percent-difference scoring system. Data for methionine processing, tran […]

library_books

Antigen Presentation Profiling Reveals Recognition of Lymphoma Immunoglobulin Neoantigens

2017
Nature
PMCID: 5808925
PMID: 28329770
DOI: 10.1038/nature21433

[…] Sequence logos for recovered MHC-I peptides were produced using Icelogo http://iomics.ugent.de/icelogoserver to reveal position weighting at anchor residues. The size distribution of recovered MHC-I and MHC-II bound peptides was compared to size distributions of known MHC-I and […]

library_books

Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome*

2016
PMCID: 5054341
PMID: 27535140
DOI: 10.1074/mcp.M116.060368

[…] no-LC-MS/MS, and data were processed as above, but with enzyme specificity set to “none” to identify peptide sequences that were generated upon calpain cleavage of denatured proteins. Icelogo (http://iomics.ugent.be/icelogoserver/main.html) was used to visualize potential consensus cleavage patterns considering four amino acids N-terminal and C-terminal of cleavage sites, i.e. positions P4-P4′ acc […]

library_books

Cysteine and Aspartyl Proteases Contribute to Protein Digestion in the Gut of Freshwater Planaria

2016
PLoS Negl Trop Dis
PMCID: 4976874
PMID: 27501047
DOI: 10.1371/journal.pntd.0004893

[…] th C18 zip-tips (Rainin) and analyzed by LC-MS/MS sequencing. Mass spectrometry and data analysis were performed as described previously []. To compare substrate specificity, iceLogo software (http://iomics.ugent.be/icelogoserver/) [] was used to generate the specificity signature for amino acids at ±4 positions adjacent to the identified cleavage site. […]

library_books

Evolution of coreceptor utilization to escape CCR5 antagonist therapy

2016
Virology
PMCID: 4913893
PMID: 27128349
DOI: 10.1016/j.virol.2016.04.010

[…] ) or iTOF (http://itol.embl.de/). V3 loop consensus sequences from two functional clusterings and their significantly different amino acid positions were computed and visualized using IceLogo (http://iomics.ugent.be/icelogoserver/index.html). The statistical significances of the differences in entropy at every nucleotide position between two samples were determined by Student's t-test. […]

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