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Bioconductor - poem

poem

This is the released version of poem; for the devel version, see poem.

POpulation-based Evaluation Metrics

Bioconductor version: Release (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: 0009-0007-6404-3244 , Pierre-Luc Germain [aut, ctb] ORCID: 0000-0003-3418-4218

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")

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")

Details biocViews ATACSeq, Clustering, DimensionReduction, GraphAndNetwork, RNASeq, SingleCell, Software, Spatial, Visualization Version 1.0.1 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License GPL (>= 3) Depends R (>= 4.1.0) Imports aricode, BiocNeighbors, BiocParallel, bluster, clevr, clue, cluster, elsa, fclust, igraph, Matrix, matrixStats, mclustcomp, methods, pdist, 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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