QUILTS 2.0 – Proteogenomic Data Integration tool

QUILTS 2.0

:: DESCRIPTION

QUILTS is a tools for creating sample specific protein sequence databased. It uses genomic and transcriptomic information to create comprehensive sample specific protein database that supports the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes.

::DEVELOPER

Laboratory of Computational Proteomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2015 Dec 2. pii: mcp.M115.056226.
An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer.
Ruggles KV et al.

BioMercator v4.2.3 – Genetic Maps and QTL Integration

BioMercator v4.2.3

:: DESCRIPTION

BioMercator is a standalone application for: (1) Displaying genetic maps and QTL through a graphical user interface. (2) Performing automatic compilations of several genetic maps through a projection process. (3) Computing meta-analysis of QTL detected in independent experiments.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BioMercator

:: MORE INFORMATION

Citation:

Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J.
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
Bioinformatics. (2004) Sep 22;20(14):2321-6.

Olivier Sosnowski, Alain Charcosset and Johann Joets.
 BioMercator V3: an upgrade of genetic map compilation and QTL meta-analysis algorithms
Bioinformatics. 2012 Aug 1;28(15):2082-3. doi: 10.1093/bioinformatics/bts313.

mixOmics 6.16.1 – Omics Data Integration Project

mixOmics 6.16.1

:: 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.

Warpgroup 0.1.0 – Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis

Warpgroup 0.1.0

:: DESCRIPTION

Warpgroup is an R package for processing chromatography-mass spectrometry data.

::DEVELOPER

Patti Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R

:: DOWNLOAD

 Warpgroup

:: MORE INFORMATION

Citation:

Warpgroup: Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis.
Mahieu NG, Spalding J, Patti GJ.
Bioinformatics. 2015 Sep 30. pii: btv564.

SePIA – RNA Sequence Processing, Integration, and Analysis

SePIA

:: DESCRIPTION

SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SePIA

:: MORE INFORMATION

Citation

SePIA: RNA and small RNA sequence processing, integration, and analysis.
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z

Mobyle 1.5.5 – Integration of Bioinformatics Software and Databanks

Mobyle 1.5.5

:: DESCRIPTION

Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks., Mobyle provides a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

Mobyle Online

::DEVELOPER

 Mobyle Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Mobyle

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Nov 15;25(22):3005-11. Epub 2009 Aug 17.
Mobyle: a new full web bioinformatics framework.
Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C.

HBN – Integration of Relational and Hierarchical Network Information for Protein Function Prediction

HBN

:: DESCRIPTION

HBN is a software of hierarchical binomial neighborhood (HBN) method for Protein Function Prediction

::DEVELOPER

Eric D. Kolaczyk

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 HBN

:: MORE INFORMATION

Citation

Jiang, X., Nariai, N., Steffen, M., Kasif, S., and Kolaczyk, E.D. (2007).
Integration of Relational and Hierarchical Network Information for Protein Function Prediction.
BMC Bioinformatics, 9:350.

Situs 3.1r2 – Integration of Multi-Resolution Structures

Situs 3.1r2

:: DESCRIPTION

Situs is a program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

::DEVELOPER

Willy Wriggers

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Situs

:: MORE INFORMATION

Citation

Willy Wriggers.
Using Situs for the Integration of Multi-Resolution Structures.
Biophysical Reviews, 2010, Vol. 2, pp. 21-27.

DynaMIT 1.1.5 – Dynamic Motif Integration Toolkit

DynaMIT 1.1.5

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

RABIT – Regression Analysis with Background InTegration

RABIT

:: DESCRIPTION

RABIT is a very efficient feature selection algorithm. It was applied to find tumor associated regulators in diverse cancer types.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RABIT

:: MORE INFORMATION

Citation

Inference of transcriptional regulation in cancers.
Jiang P, Freedman ML, Liu JS, Liu XS.
Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7731-6. doi: 10.1073/pnas.1424272112.