htsint 0.5.2 – High Throughput data Integration tool

htsint 0.5.2

:: DESCRIPTION

htsint (High-Throughput Sequencing INTegrate) is a Python package used to create gene sets for the study of high-throughput sequencing data.

::DEVELOPER

Adam J Richards

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 htsint

:: MORE INFORMATION

Citation

htsint: a Python library for sequencing pipelines that combines data through gene set generation.
Richards AJ, Herrel A, Bonneaud C.
BMC Bioinformatics. 2015 Sep 24;16(1):307.

lcmix 0.3 – R package using Hierarchical Mixture Models for Genomic data Integration

lcmix 0.3

:: DESCRIPTION

lcmix (Layered and chained mixture models) is an R package using hierarchical mixture models for genomic data integration.

::DEVELOPER

Katerina Kechris

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 lcmix 

:: MORE INFORMATION

Citation

D. Dvorkin, B. Biehs and K. Kechris (2013)
A graphical model method for integrating multiple sources of genome-scale data.
Statistical Applications in Genetics and Molecular Biology 12:469-87

MOSFLM 7.4.0 / iMOSFLM 7.3.0 – Integration of Macromolecular Diffraction Data

MOSFLM 7.4.0 / iMOSFLM 7.3.0

:: DESCRIPTION

Mosflm is a program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

iMOSFLM is a graphical user interface to the diffraction data-integration program MOSFLM. It is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. Each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user.

:: DEVELOPER

Harry Powell

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MOSFLMiMOSFLM

:: MORE INFORMATION

Citation:

Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57. Epub 2005 Dec 14.
The integration of macromolecular diffraction data.
Leslie AG.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):271-81. Epub 2011 Mar 18.
iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM.
Battye TG, Kontogiannis L, Johnson O, Powell HR, Leslie AG.

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.