smoppix - Analyze Single Molecule Spatial Omics Data Using the Probabilistic Index
Test for univariate and bivariate spatial patterns in spatial omics data with single-molecule resolution. The tests implemented allow for analysis of nested designs and are automatically calibrated to different biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.
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transcriptomicsspatialsinglecellcpp
5.52 score 1 stars 1 dependents 6 scriptspengls - Fit Penalised Generalised Least Squares models
Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.
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transcriptomicsregressiontimecoursespatial
4.30 score 4 scripts 284 downloadsoosse - Out-of-Sample R² with Standard Error Estimation
Estimates out-of-sample R² through bootstrap or cross-validation as a measure of predictive performance. In addition, a standard error for this point estimate is provided, and confidence intervals are constructed.
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4.30 score 4 stars 7 scripts 216 downloadssbivar - Test for Spatial Bivariate Association Across Omics Types
The sbivar package implements a suite of tests for Spatial BIVARiate association across omics modalities, with possibly disjoint coordinate sets. Implemented tests are generalized additive models (GAMs), modified t-test, bivariate Moran's I and Gaussian processes (GPs). Both single images and replicated experiments can be analysed.
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transcriptomicsspatialproteomicsmetabolomicsopenblascpp
4.08 score 4 scripts