CAGEfightR - Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
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softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
8.25 score 10 stars 1 dependents 133 scripts 734 downloadsnanotubes - Mouse nanotube CAGE data
Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).
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experimentdatasequencingdataexpressiondatadatapkg
4.48 score 1 dependents 3 scriptsS4Cartographer - Visualize S4 class inheritance across R/Bioconductor packages
S4 Object-Oriented Programming is fundamental to the Bioconductor ecosystem, enabling modularity and code reuse across hundreds of packages. However, the multi-layered inheritance structures within and between packages can be difficult to navigate. S4Cartographer facilitates the exploration of these relationships by visualizing S4 class hierarchies as directed graphs. By representing classes as nodes and inheritance as edges, it provides a clear overview of complex dependency networks.
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softwarevisualizationgraphandnetwork
3.48 score 1 scripts 621 downloadsCAGEWorkflow - A step-by-step guide to analyzing CAGE data using R/Bioconductor
Workflow for analyzing Cap Analysis of Gene Expression (CAGE) data using R/Bioconductor.
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geneexpressionworkflowannotationworkflow
1.30 score