DeeDeeExperiment - DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.
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softwareinfrastructuredatarepresentationgeneexpressiontranscriptiontranscriptomicsdifferentialexpressionpathwaysgo
5.62 score 1 stars 1 dependents 10 scripts 292 downloadsEMMA - EMMA: Enrichment Methods Matter for enabling fully reproducible and provenance-aware pathway analysis
EMMA is a package that provides a provenance-aware execution framework for functional enrichment analyses. It allows users to run enrichment analyses using existing tools and workflows while explicitly capturing analytical parameters during runtime, and returns the native enrichment results output together with structured metadata.
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softwarepathwaysgokegggenesetenrichmentimmunooncologytranscriptomicssinglecellgeneexpressiondifferentialexpressionbioconductorfunctional-enrichment-analysisreproducible-research
5.34 score 1 stars 88 scripts 592 downloadsiSEEfier - Streamlining the creation of initial states for starting an iSEE instance
iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user).
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cellbasedassaysclusteringdimensionreductionfeatureextractionguigeneexpressionimmunooncologyshinyappssinglecellsoftwaretranscriptiontranscriptomicsvisualization
4.30 score 3 scripts 284 downloads