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bioc
GeneTonic:Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.
Maintained by Federico Marini. Last updated 3 months ago.
guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly
77 stars 8.28 score 37 scripts 1 dependents
cran
phoenics:Pathways Longitudinal and Differential Analysis in Metabolomics
Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.
Maintained by Camille Guilmineau. Last updated 2 months ago.
2.70 score
moseleybioinformaticslab
categoryCompare2:Meta-Analysis of High-Throughput Experiments Using Feature Annotations
Facilitates comparison of significant annotations (categories) generated on one or more feature lists. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Maintained by Robert M Flight. Last updated 5 months ago.
annotationgomultiplecomparisonpathwaysgeneexpressionbioconductorbioinformaticsgene-annotationgene-expressiongene-sets
1 stars 2.30 score 9 scripts