Wrench - Wrench normalization for sparse count data
Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.
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normalizationsequencingsoftware
8.05 score 6 stars 10 dependents 30 scripts 3.5k downloadsepivizrServer - WebSocket server infrastructure for epivizr apps and packages
This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.
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infrastructurevisualization
6.07 score 5 dependents 13 scripts 431 downloadsepivizr - R Interface to epiviz web app
This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.
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visualizationinfrastructuregui
5.37 score 2 dependents 39 scripts 658 downloadsepivizrData - Data Management API for epiviz interactive visualization app
Serve data from Bioconductor Objects through a WebSocket connection.
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infrastructurevisualization
5.08 score 1 stars 4 dependents 4 scripts 564 downloadsepivizrChart - R interface to epiviz web components
This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.
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visualizationgui
4.75 score 14 scripts 526 downloadsantiProfiles - Implementation of gene expression anti-profiles
Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.
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geneexpressionclassification
3.90 score 1 scripts 520 downloadsepivizrStandalone - Run Epiviz Interactive Genomic Data Visualization App within R
This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.
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visualizationinfrastructuregui
3.30 score 4 scripts 546 downloadsantiProfilesData - Normal colon and cancer preprocessed affy data for antiProfile building.
Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package
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experimentdatamicroarraydatatissuecancerdatacoloncancerdatadatapkg
2.48 score 15 scripts