SpatialExperiment - S4 Class for Spatially Resolved -omics Data
Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.
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datarepresentationdataimportinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatialu24ca289073
13.44 score 74 stars 126 dependents 4.1k scripts 17k downloadsSpaceTrooper - SpaceTrooper performs Quality Control analysis of Image-Based spatial
SpaceTrooper performs Quality Control analysis using data driven GLM models of Image-Based spatial data, providing exploration plots, QC metrics computation, outlier detection. It implements a GLM strategy for the detection of low quality cells in imaging-based spatial data (Transcriptomics and Proteomics). It additionally implements several plots for the visualization of imaging based polygons through the ggplot2 package.
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softwaretranscriptomicsgeneexpressionqualitycontrolspatialsinglecelldataimportimmunooncology
7.96 score 13 stars 50 scripts 386 downloadseasyreporting - Helps creating report for improving Reproducible Computational Research
An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.
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reportwriting
4.60 score 2 stars 7 scripts 379 downloadsDEScan2 - Differential Enrichment Scan 2
Integrated peak and differential caller, specifically designed for broad epigenomic signals.
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immunooncologypeakdetectionepigeneticssoftwaresequencingcoveragecpp
3.30 score 4 scripts 608 downloads