TOAST - Tools for the analysis of heterogeneous tissues

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge.

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dnamethylationgeneexpressiondifferentialexpressiondifferentialmethylationmicroarraygenetargetepigeneticsmethylationarray

8.34 score 14 stars 4 dependents 120 scripts 1.1k downloads

RegionalST - Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

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spatialtranscriptomicsreactomekegg

4.18 score 8 scripts 217 downloads

caROC - Continuous Biomarker Evaluation with Adjustment of Covariates

Compute covariate-adjusted specificity at controlled sensitivity level, or covariate-adjusted sensitivity at controlled specificity level, or covariate-adjust receiver operating characteristic curve, or covariate-adjusted thresholds at controlled sensitivity/specificity level. All statistics could also be computed for specific sub-populations given their covariate values. Methods are described in Ziyi Li, Yijian Huang, Datta Patil, Martin G. Sanda (2021+) "Covariate adjustment in continuous biomarker assessment".

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2.00 score 5 scripts 183 downloads