Package: WormTensor 0.1.2

Kentaro Yamamoto

WormTensor: A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'

A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.

Authors:Kentaro Yamamoto [aut, cre], Koki Tsuyuzaki [aut], Itoshi Nikaido [aut]

WormTensor_0.1.2.tar.gz
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WormTensor_0.1.2.tgz(r-4.6-any)WormTensor_0.1.2.tgz(r-4.5-any)
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WormTensor_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
WormTensor/json (API)

# Install 'WormTensor' in R:

install.packages('WormTensor', repos = c('https://rikenbit.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rikenbit/wormtensor/issues

On CRAN:

3.70 score 1 stars 4 scripts 161 downloads 7 exports 157 dependencies

Last updated from:6cf63a315d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	286
source / vignettes	OK	306
linux-release-x86_64	OK	292
macos-release-arm64	OK	168
macos-oldrel-arm64	OK	188
windows-devel	OK	274
windows-release	OK	302
windows-oldrel	OK	243
wasm-release	OK	167

Exports:as_worm_tensor worm_clustering worm_distance worm_download worm_evaluate worm_membership worm_visualize

Dependencies:abind ade4 aricode backports base64enc BH boot broom bslib cachem car carData class cli clue cluster clusterSim clValid codetools colorspace commonmark corrplot cowplot cpp11 crosstalk dendextend Deriv digest doBy dplyr dqrng DT dtw dtwclust e1071 ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap flashClust flexclust FNN fontawesome foreach forecast Formula fracdiff fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr htmltools htmlwidgets httpuv irlba isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval leaps lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr modeltools multcompView mvtnorm nlme nloptr nnet numDeriv otel pbkrtest pillar pixmap pkgconfig plyr polynom promises proxy purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppParallel RcppProgress RcppThread Rdpack reformulas reshape2 rlang rmarkdown RSpectra rstatix rTensor Rtsne S7 sass scales scatterplot3d shiny shinyjs sitmo sourcetools sp SparseM stringi stringr survival tibble tidyr tidyselect timeDate tinytex urca usedist utf8 uwot vctrs viridis viridisLite withr xfun xtable yaml zoo

Clustering and visualization of time-series whole-brain activity data of C. elegans using WormTensor

Rendered fromWormTensor.Rmdusingknitr::rmarkdown

Last update: 2022-08-25
Started: 2022-08-03

Help page	Topics
Components for WormTensor object	AllGenerics_component worm_clustering worm_evaluate worm_membership worm_visualize
Generates WormTensor object A WormTensor object is generated from distance matrices.	as_worm_tensor
Generates clustering result A clustering result is generated from a membership tensor.	worm_clustering,WormTensor-method
Generates distance matrices Distance matrices are generated between the cells of multiple animals (Caenorhabditis elegans) from time-series matrices.	worm_distance
Downloads distance matrices 28 animals' data including 24 normal and 4 noisy are retrieved from figshare.	worm_download
Evaluates clustering result An evaluation result is generated from a WormTensor object.	worm_evaluate,WormTensor-method
Generates membership tensor A membership tensor is generated from distance matrices.	worm_membership,WormTensor-method
Plots evaluation result A visualization result is generated from a WormTensor object.	worm_visualize,WormTensor-method
S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R	WormTensor-class

Package: WormTensor 0.1.2

WormTensor: A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'

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