Predictionet 1.30.0 – Inference for Predictive Networks designed for Genomic data

Predictionet 1.30.0

:: DESCRIPTION

Predictionet contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

  Predictionet

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jan;40(Database issue):D866-75. doi: 10.1093/nar/gkr1050. Epub 2011 Nov 16.
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Haibe-Kains B1, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J.

MonaLisa r5_100 – Visualization and Analysis of Functional Modules in Biochemical Networks

MonaLisa r5_100

:: DESCRIPTION

MonaLisa is a Petri net based tool for the analysis of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques, focusing on network decomposition, knockout analysis, and other. It includes the computation of elementary modes (T-invariants), P-invariants, Maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, cluster coefficient distribution.

::DEVELOPER

Molecular Bioinformatics MolBI

:: SCREENSHOTS

MonaLisa

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MonaLisa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1469-70. doi: 10.1093/bioinformatics/btt165. Epub 2013 Apr 5.
MonaLisa–visualization and analysis of functional modules in biochemical networks.
Einloft J, Ackermann J, Nöthen J, Koch I.

ICM-Browser 3.8-7d – Molecules & Sequence Alignments Visualization

ICM-Browser 3.8-7d

:: DESCRIPTION

ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.

When you purchase the license ICM-Browser will become ICM-Browser-Pro.ICM-Browser-Pro is a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data. It allows you to read data from multiple file formats, annotate the data, and write multi-slide documents in a single small cross-platform file. ICM Browser Pro is well suited for creating, storing and sharing structural, biological and chemical information. The files can then be opened and viewed with the free ICM Browser.

::DEVELOPER

Molsoft LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/Mac OS X

:: DOWNLOAD

ICM-Browser ; Manual

:: MORE INFORMATION

RamiGO 1.20.0 – AmiGO Visualization Interface for R

RamiGO 1.20.0

:: DESCRIPTION

RamiGO is an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 RamiGO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Mar 1;29(5):666-8. doi: 10.1093/bioinformatics/bts708. Epub 2013 Jan 6.
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.
Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.

Tablet 1.19.09.03 – Next Generation Sequence Assembly Visualization

Tablet 1.19.09.03

:: DESCRIPTION

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Tablet

:: MORE INFORMATION

Citation

Milne, I, Bayer, M, Cardle, L, Shaw, P, Stephen, G, Wright, F and Marshall, D. 2010.
Tablet – next generation sequence assembly visualization.
Bioinformatics 26(3), 401-402.

PDIviz 1.2.3 – Visualization of Protein-DNA Binding Interfaces

PDIviz 1.2.3

:: DESCRIPTION

PDIviz is a plugin for the PyMOL molecular visualization system that is specifically designed to visualize protein-DNA interfaces in three dimensions. PDIviz detects the interface of protein-DNA complexes by calculating the buried surface area directly in PyMOL.

::DEVELOPER

MBL – Laboratorio de Bioinformática

:: SCREENSHOTS

PDIviz

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

  PDIviz

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 16. pii: btv203.
PDIviz: Analysis and visualization of protein-DNA binding interfaces.
Ribeiro J, Melo F, Schüller A

Gitools 2.3.1 – Analysis and Visualization of Genomic Data Using Interactive Heat-Maps

Gitools 2.3.1

:: DESCRIPTION

Gitools is a framework for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Gitools allows to import data directly from IntOGen and Biomart.

::DEVELOPER

 Gitools Team , Biomedical Genomics Group at the Biomedical Research Park in Barcelona (PRBB)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

:: DOWNLOAD

 Gitools

:: MORE INFORMATION

Citation

Perez-Llamas, C. & Lopez-Bigas, N.
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps.
PLoS ONE 6, e19541 (2011)

Genefu 3.9 – Computation of Gene Expression-Based Signatures in Breast Cancer

Genefu 3.9

:: DESCRIPTION

Genefu contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Genefu

:: MORE INFORMATION

Citation:

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693.

MCA 3.1 – Visualization method for Correlated Subpopulations

MCA 3.1

:: DESCRIPTION

MCA (Multiresolution Correlation Analysis) is a tool for the discovery of subpopulations by displaying the correlation of two genes for all possible subpopulations at once.

::DEVELOPER

Quantitative Single Cell Dynamics, Institute of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
:: DOWNLOAD

 MCA

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Jul 11;15:240. doi: 10.1186/1471-2105-15-240.
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data.
Feigelman J, Theis FJ, Marr C

JDet 1.4.9 – Visualization of Function-related Conservation Patterns in multiple Sequence Alignments

JDet 1.4.9

:: DESCRIPTION

JDet is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.

::DEVELOPER

[Computational Systems Biology Group @CNB-CSIC]

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 JDet

:: MORE INFORMATION

Citation

Thilo Muth, Juan A. Garcia-Martin, Antonio Rausell, David Juan, Alfonso Valencia & Florencio Pazos (2012).
JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.
Bioinformatics 28(4): 584-586.