poem
This is thereleased version of poem; for the devel version, seepoem.
POpulation-based Evaluation Metrics
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq,Clustering,DimensionReduction,GraphAndNetwork,RNASeq,SingleCell,Software,Spatial,Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | poem_1.2.0.tar.gz |
| Windows Binary (x86_64) | poem_1.2.0.zip |
| macOS Binary (x86_64) | poem_1.2.0.tgz |
| macOS Binary (arm64) | poem_1.2.0.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 |