Flapjack 1.22.04.21 – Graphical Genotype Visualization

Flapjack 1.22.04.21

:: DESCRIPTION

Flapjack is a new software tool for graphical genotyping and haplotype visualization which is required that can routinely handle the large data volumes generated by high throughput SNP and comparable genotyping technologies. Flapjack is a new visualization tool to facilitate analysis of these data types. Its visualizations are rendered in real-time allowing for rapid navigation and comparisons between lines, markers and chromosomes.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Flapjack

:: MORE INFORMATION

Citation

Iain Milne etc.
Flapjack – Graphical Genotype Visualization
Bioinformatics (2010)doi : 10.1093/bioinformatics/btq580

iVUN 1.2 – interactive Visualization of Uncertain Biochemical Reaction Networks

iVUN 1.2

:: DESCRIPTION

iVUN is a visualization toolbox which supports uncertainty-aware analysis of static and dynamic attributes of biochemical reaction networks

::DEVELOPER

iVUN Team

:: SCREENSHOTS

iVUN

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 iVUN

:: MORE INFORMATION

Citation

C. Vehlow, J. Hasenauer, A. Kramer, J. Heinrich, N. Radde, F. Allgoewer, and D. Weiskopf.
Uncertainty-aware visual analysis of biochemical reaction networks.
In Proceedings of IEEE Symposium on Biological Data Visualization(Biovis), pages 91–98, 2012.

CMView 1.1.1 – Protein Contact Map Visualization and Analysis

CMView 1.1.1

:: DESCRIPTION

CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.

::DEVELOPER

CMView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 CMView

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1573-4. Epub 2011 Apr 5.
CMView: interactive contact map visualization and analysis.
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M.

PIVOT v1.0.1 – Platform for Interactive analysis and Visualization Of Transcriptomics data

PIVOT v1.0.1

:: DESCRIPTION

PIVOT is an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

PIVOT

:: MORE INFORMATION

Citation

Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J.
PIVOT: platform for interactive analysis and visualization of transcriptomics data.
BMC Bioinformatics. 2018 Jan 5;19(1):6. doi: 10.1186/s12859-017-1994-0. PMID: 29304726; PMCID: PMC5756333.

QuantileMap – Visualization of Compactlydemonstrate Multiple Distributions in Genomic Applications

QuantileMap

:: DESCRIPTION

QuantileMap is a visualization tool to compactlydemonstrate multiple (hundreds) distributions in genomic applications.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QuantileMap

:: MORE INFORMATION

Citation

George C. Tseng. (2009)
Quantile map: Simultaneous visualization of patterns in many distributions with application to tandem mass spectrometry.
Comput Stat Data Anal. 2010 April 1; 54(4): 1124.

ViDaExpert 1.2 – Multidimensional Vectorial data Visualization

ViDaExpert 1.2

:: DESCRIPTION

ViDaExpert (VIsualization of DAta) is a software for multidimensional vectorial data visualization (ViDa stands for VIsualization of DAta). ViDaExpert was shown to be a useful tool, in particular, in analysis of microarray data. There are special panels integrated to support analysis of microarray data (for example, dot-plots). In Sitcon project it is used to perform PCA analysis of microarray data, including time series.

::DEVELOPER

Andrei Zinovyev

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ViDaExpert

:: MORE INFORMATION

References

  1. Gorban A., Zinovyev A. Elastic Principal Graphs and Manifolds and their Practical Applications. Computing, 2005 (PDF)
  2. Andrei Zinovyev. Method And Software For Fast Construction Of Principal Manifolds Approximations. (PDF)
  3. Alexander Gorban, Andrei Zinovyev. Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology. (PDF)
  4. Alexander Gorban, Andrei Zinovyev and Donald Wunsch. Application of the method of elastic maps in analysis of genetic texts. (PDF)

RNA-Scoop v1.0.1 – Interactive Visualization of Single-cell Transcriptomes

RNA-Scoop v1.0.1

:: DESCRIPTION

RNA Scoop is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive cell cluster plot, users are able to explore isoforms in a single-cell transcriptome dataset of thousands of cells.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE

:: DOWNLOAD

RNA Scoop

:: MORE INFORMATION

Citation

Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I.
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes.
NAR Genom Bioinform. 2021 Nov 29;3(4):lqab105. doi: 10.1093/nargab/lqab105. PMID: 34859209; PMCID: PMC8633890.

ViTraM 2.0 – Visualization of Transcriptional Modules

ViTraM 2.0

:: DESCRIPTION

ViTraM (Visualization of Transcriptional Modules) is a flexible software platform for visualizing overlapping transcriptional modules in an intuitive way. By visualizing not only the genes and the experiments in which the genes are co-expressed, but also additional properties of the modules such as the regulators and regulatory motifs that are responsible for the observed co-expression, ViTraM can assist in the biological analysis and interpretation of the output of module detection tools.

::DEVELOPER

Kathleen Marchal

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 ViTraM

:: MORE INFORMATION

Citation

H. Sun, K. Lemmens, T. Van den Buckle, K. Engelen, B. De Moor, K. Marchal.
ViTraM: Visualization of Transcriptional Modules” (2009).
Bioinformatics, 25(18):2450-2451;

ProteoVision – Advanced Visualization of (Ribosomal) Proteins

ProteoVision

:: DESCRIPTION

ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures.

::DEVELOPER

ProteoVision team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS.
ProteoVision: web server for advanced visualization of ribosomal proteins.
Nucleic Acids Res. 2021 Jul 2;49(W1):W578-W588. doi: 10.1093/nar/gkab351. PMID: 33999189; PMCID: PMC8265156.

matrix2png 1.2.2 – Visualization tool for Display of Matrix data

matrix2png 1.2.2

:: DESCRIPTION

matrix2png is a visualization tool for the display of matrix data.Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows with Cygwin

:: DOWNLOAD

 matrix2png

:: MORE INFORMATION

Citation

Pavlidis, P. and Noble W.S. (2003)
Matrix2png: A Utility for Visualizing Matrix Data.
Bioinformatics 19: 295-296