poem
This is the released version of poem; for the devel version, see poem.
POpulation-based Evaluation Metrics
Bioconductor version: Release (3.23)
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]
, Pierre-Luc Germain [aut, ctb]
Maintainer: Siyuan Luo <roseluosy at gmail.com>
citation("poem")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| 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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | poem_1.4.0.tar.gz |
| Windows Binary (x86_64) | poem_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | poem_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | poem_1.4.0.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 |