Table 8.
Microarray and RNAseq analysis viewers
| Tool and references | Description | URL |
|---|---|---|
| ArrayXPath [201] | Mapping and visualizing microarray gene-expression data with integrated biological pathway resources using scalable vector graphics | http://www.snubi.org/software/ArrayXPath/ |
| BicOverlapper [301, 302] | Supports visual analysis of gene expression by means of biclustering | http://vis.usal.es/bicoverlapper/ |
| BiGGEsTS [303] | Tool providing an integrated environment for the biclustering analysis of time-series gene-expression data | http://tinyurl.com/BiGGEsTS/ |
| eRNA [304] | RNA data analysis tool for high-throughput RNA sequencing experiments | https://sourceforge.net/projects/erna/?source=directory |
| EXPANDER [130] | A Java-based tool for analysis of gene-expression and NGS data | http://acgt.cs.tau.ac.il/expander/ |
| ExpressionProfiler [305] | Web-based platform for microarray gene-expression and other functional-genomics-related data analysis | http://www.ebi.ac.uk/expressionprofiler |
| GenePattern [129] | Modular analysis web platform; several visualization modules available | http://genepattern.broadinstitute.org/gp/pages/login.jsf |
| Genesis [128] | Java package of tools to simultaneously visualize and analyze a whole set of gene-expression experiments | http://genome.tugraz.at/genesisclient/genesisclient_description.shtml |
| GeneVAnD [306] | Linked heatmaps, dendrograms and 2D/3D scatter plots | http://tinyurl.com/GeneVAnD/ |
| geWorkbench [307] | A Java-based open-source platform for integrated genomics. It allows individually developed plugins to be configured into complex bioinformatic applications. Currently more than 70 available plugins supporting the visualization and analysis | http://wiki.c2b2.columbia.edu/workbench/index.php/Home |
| Gitools [308] | Analysis and visualization of genomic data using interactive heatmaps | http://www.gitools.org |
| HCE [309] | Linked heat map, profile and scatter plots; systematic exploration | http://www.cs.umd.edu/hcil/hce/ |
| HeatmapGenerator [310] | Create customized gene-expression heatmaps from RNAseq and microarray data | http://sourceforge.net/projects/heatmapgenerator/ |
| HeatMapViewer [311] | Interactive display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants | http://dx.doi.org/10.5281/zenodo.7706 |
| Mayday [312] | A graphical user interface that supports the development and integration of existing and new analysis methods. Many linked visualizations | http://it.informatik.uni-tuebingen.de/?page_id=248/wp/ |
| MultiExperiment Viewer [127] | Analysis suite. Heatmaps, dendrograms, profile and scatter plots | http://www.tm4.org/ |
| PointCloudXplore [313] | Visualization of transcription data in Drosophila embryos. Multiple views to ease analysis of complex gene-expression data. This type of interaction blends high-dimensional information exploration with interactive, 3D visualization | http://tinyurl.com/PointCloudXplore/ |
| RNASeqBrowser [314] | A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks | http://www.australianprostatecentre.org/research/software/rnaseqbrowser |
| RNAseqViewer [315] | Visualization of the various data from the RNAseq analyzing process, for single or multiple samples | http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/ |
| TimeSearcher [316] | Interactive querying and exploration of time-series data | http://www.cs.umd.edu/hcil/timesearcher/ |
| TraV [317] | Visualization and analysis of multiple transcriptome sequencing experiments | http://appmibio.uni-goettingen.de/index.php?sec=serv |