poem
A package containing metrics for evaluating subpopulation identification in clusterings, embeddings, graphs and space.
Science Score: 26.0%
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Low similarity (10.3%) to scientific vocabulary
Repository
A package containing metrics for evaluating subpopulation identification in clusterings, embeddings, graphs and space.
Basic Info
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
poem: POpulation-based Evaluation Metrics
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Overview
The poem package provides multiple metrics for evaluating subpopulation structure identification in a dataset. These include:
Metrics for comparing two partitions[^1] of the same dataset, or metrics evaluating the alignment between a dataset’s embedding or graph representations with its partition.
Metrics for comparing two fuzzy partitions[^2], or for comparing a hard partition with a fuzzy partition. This allows the evaluation of fuzzy partition results by assessing its agreement to a fuzzy or a hard ground-truth partition.
Metrics tailored for domain detection in spatially-resolved omics data. These include especially external evaluation metrics (i.e. based on a comparison to ground truth labels), but also internal metrics.
[^1]: A partition is a way of organizing the data points of a dataset into distinct, non-overlapping, and non-empty subsets. For example, a clustering is a partition.
[^2]: In 'hard' partitions, each data point belongs to one and only one subset. However, clustering can also generate fuzzy partitions, in which data points can belong to multiple subsets with varying degrees (or probability) of membership.
For a detailed introduction of the package, see the online docs.
Installation
poem is available through Bioconductor, and can be installed using the following commands:
r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("poem")
Contact
In case you have any questions or suggestions to poem, please consider opening an
issue to the GitHub repository.
Owner
- Name: Siyuan Luo
- Login: RoseYuan
- Kind: user
- Repositories: 1
- Profile: https://github.com/RoseYuan
GitHub Events
Total
- Watch event: 10
- Push event: 132
- Create event: 3
- Commit comment event: 1
Last Year
- Watch event: 10
- Push event: 132
- Create event: 3
- Commit comment event: 1
Packages
- Total packages: 1
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Total downloads:
- bioconductor 1,331 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: poem
POpulation-based Evaluation Metrics
- Homepage: https://roseyuan.github.io/poem/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/poem/inst/doc/poem.pdf
- License: GPL (>= 3)
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Latest release: 1.0.1
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v2 composite
- actions/upload-artifact master composite
- R >= 4.0 depends
- BiocNeighbors * imports
- BiocParallel * imports
- Matrix * imports
- aricode * imports
- bluster * imports
- clevr * imports
- clue * imports
- cluster * imports
- elsa * imports
- fclust * imports
- igraph * imports
- mclustcomp * imports
- methods * imports
- sp * imports
- spdep * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- DT * suggests
- cowplot * suggests
- dplyr * suggests
- ggnetwork * suggests
- ggplot2 * suggests
- knitr * suggests
- scico * suggests
- testthat >= 3.0.0 suggests
- tidyr * suggests
- bioconductor/bioconductor_docker devel build
- actions/checkout v4 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite