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WebGestaltR - Gene Set Analysis Toolkit WebGestaltR

The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

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rustcargo

9.03 score 38 stars 283 scripts 891 downloads

NetSAM - Network Seriation And Modularization

The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.

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softwaregraphandnetworknetworknetworkinferenceclusteringgeneexpressionvisualizationgogenesetenrichmentsystemsbiology

4.18 score 1 scripts 500 downloads

clinicalomicsdbR - Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data Downloading and Importing

Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.

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3.30 score 4 stars 370 downloads