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poem

This is the development version of poem; to use it, please install the devel version of Bioconductor.

POpulation-based Evaluation Metrics


Bioconductor version: Development (3.21)

This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.

Author: Siyuan Luo [cre, aut] (ORCID: ), Pierre-Luc Germain [aut, ctb] (ORCID: )

Maintainer: Siyuan Luo <roseluosy at gmail.com>

Citation (from within R, enter citation("poem")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("poem")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("poem")
1_introduction HTML R Script
3_SpatialExperiment HTML R Script
MetricsInPoem.html HTML R Script
Reference Manual PDF

Details

biocViews ATACSeq, Clustering, DimensionReduction, GraphAndNetwork, RNASeq, SingleCell, Software, Spatial, Visualization
Version 0.99.7
In Bioconductor since BioC 3.21 (R-4.5)
License GPL (>= 3)
Depends R (>= 4.1.0)
Imports aricode, BiocNeighbors, BiocParallel, bluster, clevr, clue, cluster, elsa, fclust, igraph, Matrix, mclustcomp, methods, sp, spdep, stats, utils, SpatialExperiment, SummarizedExperiment
System Requirements
URL https://roseyuan.github.io/poem/
Bug Reports https://github.com/RoseYuan/poem/issues
See More
Suggests testthat (>= 3.0.0), BiocStyle, knitr, DT, dplyr, kableExtra, scico, cowplot, ggnetwork, ggplot2, tidyr, STexampleData
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package poem_0.99.7.tar.gz
Windows Binary (x86_64) poem_0.99.7.zip
macOS Binary (x86_64) poem_0.99.7.tgz
macOS Binary (arm64) poem_0.99.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/poem
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/poem
Bioc Package Browser https://code.bioconductor.org/browse/poem/
Package Short Url https://bioconductor.org/packages/poem/
Package Downloads Report Download Stats