VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

expVIP 20180914 – RNA-seq Data Analysis and Visualization Platform

expVIP 20180914

:: DESCRIPTION

ExpVIP (expression visualization and integration platfor) is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

expVIP

:: MORE INFORMATION

Citation

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.
Borrill P, Ramirez-Gonzalez R, Uauy C.
Plant Physiol. 2016 Apr;170(4):2172-86. doi: 10.1104/pp.15.01667.

BatMass 0.3.1 – Mass Spectrometry data Visualization

BatMass 0.3.1

:: DESCRIPTION

BatMass is a mass-spectrometry data visualization tool, with the main focus on being fast and interactive while providing comprehensive visualizations without any parameter tweaking.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

BatMass

:: MORE INFORMATION

Citation:

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.
BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.
Avtonomov DM, Raskind A, Nesvizhskii AI.

IOBIO – Realtime Genomic Data Visualization and Analysis Web Tools

IOBIO

:: DESCRIPTION

Iobio provides free and open-source tools that help to generate gene list, variant interrogation, and more!

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

IOBIO

:: MORE INFORMATION

Citation

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools.
Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT.
J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.

ZENBU 2.11.2 – Data Integration, Data Processing, and Visualization Web system

ZENBU 2.11.2

:: DESCRIPTION

ZENBU is a data integration, data processing, and visualization web system based around three main web interfaces : an expression data enhanced genome browser interface, a secured user system for data upload and secured data sharing, and a data explorer interface to find and manipulate data across the many supported experimental data types and to find shared user configurations

::DEVELOPER

 FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux
  • web2.0 client/server
  • Java
  • c++ server infrastructure

:: DOWNLOAD

 ZENBU

:: MORE INFORMATION

Citation

Severin et al. (2014)
Interactive visualization and analysis of large-scale NGS data-sets using ZENBU.
Nat Biotechnol. 2014 Mar;32(3):217-9. doi: 10.1038/nbt.2840.

Sircah 1.0 – Detection and Visualization of Alternative Transcripts

Sircah 1.0

:: DESCRIPTION

Sircah is an application written in python that dectects and visualises alternative splicing events using spliced alignments.Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription. Such transcript models may come from the gene prediction pipelines of genome databases or from spliced alignments of ESTs or proteins against the genome.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Sircah

:: MORE INFORMATION

Citation

Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington ED, Bork P.
Bioinformatics. 2008 Sep 1;24(17):1959-60. Epub 2008 Jul 17.

 

ChIPseeker 1.22.0 – ChIP peak Annotation, Comparison & Visualization

ChIPseeker 1.22.0

:: DESCRIPTION

ChIPseeker is an R package for annotating ChIP-seq data analysis.

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 ChIPseeker

:: MORE INFORMATION

Citation:

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Yu G, Wang LG, He QY.
Bioinformatics. 2015 Mar 11. pii: btv145.

TimeScape – Visualization tool for temporal Clonal Evolution

TimeScape

:: DESCRIPTION

TimeScape is a visualization tool for temporal clonal evolution.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

TimeScape

:: MORE INFORMATION

CellScape 0.99.3 – Visualization tool for integrating single Cell Phylogeny

CellScape 0.99.3

:: DESCRIPTION

CellScape is a visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

CellScape

:: MORE INFORMATION

Clustergrammer 1.19.5 – Web-based Heatmap Visualization and Analysis Tool for High-Dimensional Biological Data

Clustergrammer 1.19.5

:: DESCRIPTION

Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Clustergrammer

:: MORE INFORMATION

Citation

Sci Data. 2017 Oct 10;4:170151. doi: 10.1038/sdata.2017.151.
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data.
Fernandez NF, Gundersen GW, Rahman A, Grimes ML, Rikova K, Hornbeck P, Ma’ayan A.