NetworkAnalyst

-- a visual analytics platform for comprehensive gene expression profiling & meta-analysis

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Starting from a list of gene IDs with optional expression values

Starting from a single count table (RNAseq) or intensity table (microarray)

Starting with several gene expression tables for meta-analysis

Uploading RNAseq fastq files to our Galaxy server for mapping & quantification

Starting with a network file (sif, graphml, json)

News & Updates

Updated R from 3.5.1 to the latest version (3.6.1) (10/16/2019);
The volcano plot now supports enrichment analysis against user defined gene sets (10/07/2019);
Fixed the broken link in meta-analysis result download page (09/18/2019);
Bug fixes - GSEA and uploading multiple list files are working now (06/24/2019);
Enhanced graphML parsing for network file upload (05/31/2019);
Updated web framework to PrimeFaces 7.0 (05/18/2019);
Updated KEGG pathways for all 17 species (04/30/2019);
Fixed the issue with PCA 3D visual analytics (04/05/2019);
Fixed the issue with DE analysis for species not in the list of the 17 organisms (03/28/2019);
Our NetworkAnalyst 3.0 manuscript is accepted by Nucleic Acids Research! (03/23/2019);
Added support for WormBase ID for C. elegans (03/22/2019);
Users can now upload gene list file(s) in addition to direct copy-and-paste (03/18/2019);
Fixed issue with box plot display when clicking a data point in volcano plot (03/12/2019);
Fixed issue with meta-data upload and table display (03/06/2019);
Updated FAQs and Tutorials based on new features (02/01/2019);
Added support for heatmap visual analytics for gene lists (01/23/2019);

Read more ......

Zhou, G., Soufan, O., Ewald, J., Hancock, REW, Basu, N. and Xia, J. (2019) "NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis" Nucleic Acids Research (doi:10.1093/nar/gkz240)
Xia J, Gill E, and Hancock REW (2015) "NetworkAnalyst for Statistical, Visual and Network-based Approaches for Meta-analysis of Expression Data" Nature Protocols 10, 823–844
Xia J, Benner MJ, and Hancock REW (2014) "NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration" Nucl. Acids Res. 42 (W1): W167-W174. (PPI data analysis and visualization)
Xia, J., Lyle, N.H., Mayer, M., Pena, O.M. and Hancock, R.E.W. (2013) “INVEX - a web-based tool for integrative visualization of expression data”. Bioinformatics 29 (24), 3232-3234 (gene expression data analysis)
Xia, J., Fjell, C.D., Mayer, M., Pena, O.M., Wishart, D.S. and Hancock, R.E.W. (2013) “INMEX - a web-based tool for integrative meta-analysis of expression data”. Nucleic Acids Research 41, W63-W70. (meta-analysis)