Package: leiden 0.4.3.1

leiden: R Implementation of Leiden Clustering Algorithm

Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arxiv:1810.08473>.

Authors:S. Thomas Kelly [aut, cre, trl], Vincent A. Traag [com]

leiden_0.4.3.1.tar.gz
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leiden_0.4.3.1.tgz(r-4.6-any)leiden_0.4.3.1.tgz(r-4.5-any)
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leiden_0.4.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
leiden/json (API)

# Install 'leiden' in R:
install.packages('leiden', repos = c('https://tomkellygenetics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tomkellygenetics/leiden/issues

On CRAN:

Conda:

9.04 score 44 stars 3 packages 291 scripts 3.8k downloads 1 exports 20 dependencies

Last updated from:22ae49d7bb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK187
source / vignettesOK317
linux-release-x86_64OK175
macos-release-arm64OK204
macos-oldrel-arm64OK204
windows-develOK326
windows-releaseOK218
windows-oldrelOK241
wasm-releaseOK143

Exports:leiden

Dependencies:clicpp11gluehereigraphjsonlitelatticelifecyclemagrittrMatrixpkgconfigpngrappdirsRcppRcppTOMLreticulaterlangrprojrootvctrswithr

Benchmarking the Leiden algorithm with R and Python
Benchmarking the Leiden Algorithm | Clustering with the Leiden Algorithm in R | Set up the python version to be called in R | Python implementation | Running in Python | Benchmarking the Python version with reticulate | R implementation | Running in R via reticulate and igraph | Calling python in R via reticulate | Calling C in R with igraph | Benchmarking the R version with reticulate | Large adjacency matrices | Comparing the adjacency matrix calling | Benchmarking C in R with igraph | Summary
Rendered frombenchmarking.Rmdusingknitr::knitr

Last update: 2023-11-08
Started: 2019-07-13

Running the Leiden algorithm with R on multiplex graphs
Clustering with the Leiden Algorithm on Multiplex Graphs | Set up | Usage | Multiplex graph objects | Running the Leiden algorithm in R | Fine-tuning with resolution | Fine-tuning with maximum community size | Multiplex cost functions
Rendered fromrun_multiplex.Rmdusingknitr::knitr

Last update: 2023-11-08
Started: 2020-12-06

Running the Leiden algorithm with R on adjacency matrices
Clustering with the Leiden Algorithm in R | Install | Usage | Running the Leiden algorithm in R | Running Leiden with arguments passed to leidenalg | Running on a Seurat Object | Seurat version 2 | Seurat version 3 or later
Rendered fromrun_leiden.Rmdusingknitr::knitr

Last update: 2022-09-12
Started: 2019-01-25

Running the Leiden algorithm with R on Graph Objects
Clustering with the Leiden Algorithm in R | Install | Usage | Running the Leiden algorithm in R | Running Leiden with arguments passed to leidenalg | Running on a Seurat Object | Seurat version 2 | Seurat version 3 or later
Rendered fromrun_igraph.Rmdusingknitr::knitr

Last update: 2021-07-27
Started: 2019-07-13

Running the Leiden algorithm with R on bipartite graphs
Clustering with the Leiden Algorithm on Bipartite Graphs | Set up | Usage | Bipartite graph objects | Running the Leiden algorithm in R | Bipartite cost functions | Resolution Parameter | Maximum Community Size Parameter | Equivalence of cost functions
Rendered fromrun_bipartite.Rmdusingknitr::knitr

Last update: 2021-01-26
Started: 2020-10-28