PINCAGE – Probabilistic INTegration of CAncer GEnomics data

PINCAGE

:: DESCRIPTION

PINCAGE is a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies.

::DEVELOPER

PINCAGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

  PINCAGE

:: MORE INFORMATION

Citation

PINCAGE: Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification.
Świtnicki MP, Juul M, Madsen T, Sørensen KD, Pedersen JS.
Bioinformatics. 2016 Jan 6. pii: btv758.

RECOG 1.1.32 – Research Environment for Comparative Genomics

RECOG 1.1.32

:: DESCRIPTION

RECOG is a workbench software program which is used to conduct comparative genome analyses on a massive scale. The main feature of RECOG is the function of ortholog analysis between genomes of numerous species based on the display of an ortholog table (rows: ortholog groups; columns: species).RECOG can also conduct various comparative analyses for detailed examination, based on this table.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

  RECOG

:: MORE INFORMATION

EDGAR 2.0 – software platform for comparative Genomics

EDGAR 2.0

:: DESCRIPTION

EDGAR (Efficient Database framework for comparative Genome Analyses using BLAST score Ratios) is designed to automatically perform genome comparisons in a high throughput approach.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Pühler A, Vorh?lter FJ, Zakrzewski M, Goesmann A.
BMC Bioinformatics. 2009 May 20;10:154. doi: 10.1186/1471-2105-10-154.

geWorkbench 2.6.0.3 – Open-source Platform for Integrated Genomics

geWorkbench 2.6.0.3

:: DESCRIPTION

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data.

::DEVELOPER

Center for Computational Biology & Bioinformatics, Columbia University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 geWorkbench

:: MORE INFORMATION

Citation:

Floratos A, Smith K, Ji Z, Watkinson J, Califano A. (2010).
geWorkbench: an open source platform for integrative genomics.
Bioinformatics 26(14):1779-80. Epub 2010 May 28.

caOmicsV 1.20.0 – Visualization of Multi-dimentional Cancer Genomics data

caOmicsV 1.20.0

:: DESCRIPTION

caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.

::DEVELOPER

Henry Zhang <hzhang at mail.nih.gov>

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R / BioConductor

:: DOWNLOAD

 caOmicsV

:: MORE INFORMATION

Citation

caOmicsV: an R package for visualizing multidimensional cancer genomic data.
Zhang H, Meltzer PS, Davis SR.
BMC Bioinformatics. 2016 Mar 22;17(1):141. doi: 10.1186/s12859-016-0989-6.

PREDA 1.32.0 – Detecting Regional Variations in Genomics data

PREDA 1.32.0

:: DESCRIPTION

PREDA (Position RElated Data Analysis) is an R package for detecting regional variations in genomics data.

::DEVELOPER

Bicciato Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 PREDA

:: MORE INFORMATION

Citation

PREDA: an R-package to identify regional variations in genomic data.
Ferrari F, Solari A, Battaglia C, Bicciato S.
Bioinformatics. 2011 Sep 1;27(17):2446-7. doi: 10.1093/bioinformatics/btr404.

KNOWENG – Knowledge Engine for Genomics

KNOWENG

:: DESCRIPTION

KnowEnG enables knowledge-guided machine learning and graph mining analysis on genomic datasets using scalable cloud computation and exploration of results with interactive visualizations.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

KnowEnG: a knowledge engine for genomics.
Sinha S, Song J, Weinshilboum R, Jongeneel V, Han J.
J Am Med Inform Assoc. 2015 Nov;22(6):1115-9. doi: 10.1093/jamia/ocv090.

CGAT Apps 0.4.0 – Scripts for Genomics and Next-generation Sequencing Analysis

CGAT Apps 0.4.0

:: DESCRIPTION

The CGAT App contains scripts and pipelines developed by CGAT. The collection contains scripts for genomics and next-generation sequencing analysis, but also general purpose scripts.

::DEVELOPER

Computational Genomics: Analysis and Training (GCAT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

CGAT Apps

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1290-1. doi: 10.1093/bioinformatics/btt756. Epub 2014 Jan 5.
CGAT: computational genomics analysis toolkit.
Sims D1, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A.

Trebol 20111212 – Interactive Comparative Genomics Tool

Trebol 20111212

:: DESCRIPTION

Trebol is a multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality images for scientific publications.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Trebol

:: MORE INFORMATION