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bioc
CATALYST:Cytometry dATa anALYSis Tools
CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.
Maintained by Helena L. Crowell. Last updated 4 months ago.
clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization
67 stars 10.99 score 362 scripts 2 dependentsbioc
spillR:Spillover Compensation in Mass Cytometry Data
Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.
Maintained by Marco Guazzini. Last updated 5 months ago.
flowcytometryimmunooncologymassspectrometrypreprocessingsinglecellsoftwarestatisticalmethodvisualizationregression
4.30 score 3 scripts