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bioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 14 days ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
22 stars 8.59 score 69 scriptsbioc
SplicingFactory:Splicing Diversity Analysis for Transcriptome Data
The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.
Maintained by Endre Sebestyen. Last updated 5 months ago.
transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing
4 stars 5.20 score 1 scripts
edsandorf
obfuscatoR:Obfuscation Game Designs
When people make decisions, they may do so using a wide variety of decision rules. The package allows users to easily create obfuscation games to test the obfuscation hypothesis. It provides an easy to use interface and multiple options designed to vary the difficulty of the game and tailor it to the user's needs. For more detail: Chorus et al., 2021, Obfuscation maximization-based decision-making: Theory, methodology and first empirical evidence, Mathematical Social Sciences, 109, 28-44, <doi:10.1016/j.mathsocsci.2020.10.002>.
Maintained by Erlend Dancke Sandorf. Last updated 2 years ago.
2 stars 4.00 score 5 scripts
cran
phiDelta:Tool for Phi Delta Analysis of Features
Analysis of features by phi delta diagrams. In particular, functions for reading data and calculating phi and delta as well as the functionality to plot it. Moreover it is possible to do further analysis on the data by generating rankings. For more information on phi delta diagrams, see also Giuliano Armano (2015) <doi:10.1016/j.ins.2015.07.028>.
Maintained by Ursula Neumann. Last updated 7 years ago.
1.00 score