BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data

BioMet Toolbox 2.0

:: DESCRIPTION

The BioMet ToolBox is a web-based resource for exploiting the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, powered by RAVEN, gene set analysis and basic microarray analysis using PIANO, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, V?remo L, Nookaew I, Nielsen J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371.

mixOmics 5.2.0 – Omics Data Integration Project

mixOmics 5.2.0

:: DESCRIPTION

mixOmics analyses highly dimensional data sets: regularized Canonical Correlation Analysis (‘rCCA’) and sparse Partial Least Squares variants (‘sPLS’) to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n.

::DEVELOPER

mixOmics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 mixOmics

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Dec 6;13:325. doi: 10.1186/1471-2105-13-325.
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.
Liquet B1, Lê Cao KA, Hocini H, Thiébaut R.

NetGestalt / NetSAM 1.10.0 – Integrating Multidimensional Omics data over Biological Networks

NetGestalt / NetSAM 1.10.0

:: DESCRIPTION

NetGestalt is a data integration framework that allows simultaneous presentation of large-scale experimental and annotation data from various sources in the context of a biological network to facilitate data visualization, analysis, interpretation, and hypothesis generation.

NetSAM (Network Seriation and Modularization) is an R package that takes an edge-list representation of a network as an input and generates files that can be used as an input for the one-dimensional network visualization tool NetGestalt  or other network analysis.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 NetSAM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):597-8. doi: 10.1038/nmeth.2517.
NetGestalt: integrating multidimensional omics data over biological networks.
Shi Z, Wang J, Zhang B.

MT-HESS 0.3 – Simultaneous Association Detection in OMICS Datasets

MT-HESS 0.3

:: DESCRIPTION

MT-HESS is a Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.

::DEVELOPER

MT-HESS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOSX

:: DOWNLOAD

 MT-HESS

:: MORE INFORMATION

Citation

MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.
Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S.
Bioinformatics. 2015 Oct 26. pii: btv568

CARMO v1.0 – Comprehensive Annotation of Rice Multi-Omics

CARMO v1.0

:: DESCRIPTION

CARMO is a web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies.

::DEVELOPER

Plant Bioinformatics and Functional Epigenomics Group, SIPPE, SIBS, CAS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.
Wang J, Qi M, Liu J, Zhang Y.
Plant J. 2015 Jul;83(2):359-74. doi: 10.1111/tpj.12894.

KeyPathwayMiner 4.0 – Combining networks with OMICS data

KeyPathwayMiner 4.0

:: DESCRIPTION

KeyPathwayMiner is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types.

::DEVELOPER

the Computational Biology research group of Jan Baumbach at the University of Southern Denmark.

:: SCREENSHOTS

KeyPathwayMiner

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 KeyPathwayMiner

:: MORE INFORMATION

Citation

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AG, Azevedo V, Ditzel HJ, Baumbach J.
BMC Syst Biol. 2014 Aug 19;8:99. doi: 10.1186/s12918-014-0099-x.

Oasys 1.0 – A Graphical Genomic Viewer for Omics Data

Oasys 1.0

:: DESCRIPTION

OASYS is a free java application tool devoted to the graphical visualization of omics measurements (SNP, gene expression, miRNA, methylome, …)

::DEVELOPER

Cartes d’Identite des Tumeurs (CIT)

:: SCREENSHOTS

Oasys

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Oasys

:: MORE INFORMATION

Citation

Anne-Sophie Valin, Laetitia Marisa, Laure Vescovo, Emilie Thomas, Mickael Guedj, Renaud Schiappa, Julien Laffaire, Fabien Petel, and Aurélien de Reyniès.
“OASYS : A graphical genomic viewer for omics data”
submission in process

dnet 1.0.6 – Integrative Analysis of Omics data in terms of Network, Evolution and Ontology

dnet 1.0.6

:: DESCRIPTION

dnet is an open-source R package for omics data integrative analysis in terms of network, evolution and ontology

::DEVELOPER

Computational Genomics Group, Department of Computer Science, University of Bristol, UK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dnet

:: MORE INFORMATION

Citation:

Genome Med. 2014 Aug 26;6(8):64. doi: 10.1186/s13073-014-0064-8. eCollection 2014.
The ‘dnet’ approach promotes emerging research on cancer patient survival.
Fang H, Gough J

supraHex 1.6.0 – Tabular Omics data analysis using a Supra-hexagonal Map

supraHex 1.6.0

:: DESCRIPTION

supraHex is an open-source R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map

::DEVELOPER

Computational Genomics Group, Department of Computer Science, University of Bristol, UK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 supraHex

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2014 Jan 3;443(1):285-9. doi: 10.1016/j.bbrc.2013.11.103. Epub 2013 Dec 2.
supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.
Fang H, Gough J

ChIP-Array 2 – Integrating multiple Omics data to construct Gene Regulatory Networks

ChIP-Array 2

:: DESCRIPTION

ChIP-Array integrates additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components.

::DEVELOPER

Bioinformatics Group, HKU Department of Biochemistry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J.
Nucleic Acids Res. 2015 Apr 27. pii: gkv398.