Tag: Genomics

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

Scribl 1.1.4 – HTML5 Canvas Genomics Graphic Library

Scribl 1.1.4

:: DESCRIPTION

Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.

::DEVELOPER

the Meyer Lab 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

  Scribl

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 1;29(3):381-3. doi: 10.1093/bioinformatics/bts677. Epub 2012 Nov 19.
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.
Miller CA, Anthony J, Meyer MM, Marth G.

atBioNet – Network Analysis Tool for Genomics and Proteomics

atBioNet

:: DESCRIPTION

atBioNet is a free, user friendly, web-based network analysis tool for analyzing, visualizing, and interpreting genomics or proteomics data. The user supplies atBioNet with a list of proteins or genes, and atBioNet then creates an interactive graphical network model that can identify key functional modules. Pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) is directly integrated within atBioNet for enrichment analysis and assessment of the biological meaning of modules.

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

 REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 atBioNet

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 20;13(1):325. [Epub ahead of print]
atBioNet – an integrated network analysis tool for genomics and biomarker discovery.
Ding Y, Chen M, Liu Z, Ding D, Ye Y, Zhang M, Kelly R, Guo L, Su Z, Harris SC, Qian F, Ge W, Fang H, Xu X, Tong W.