Package: WormTensor 0.1.1

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_0.1.1.tar.gz
WormTensor_0.1.1.tar.gz(r-4.5-noble)WormTensor_0.1.1.tar.gz(r-4.4-noble)
WormTensor_0.1.1.tgz(r-4.4-emscripten)WormTensor_0.1.1.tgz(r-4.3-emscripten)
WormTensor.pdf |WormTensor.html✨
WormTensor/json (API)
NEWS

# Install 'WormTensor' in R:

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

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

7 exports 0.00 score 148 dependencies 3 scripts 308 downloads

Last updated 2 months agofrom:47e2463de5. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 23 2024
R-4.5-linux	OK	Aug 23 2024

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 crayon crosstalk dendextend Deriv digest doBy dplyr dqrng DT dtw dtwclust e1071 ellipse emmeans estimability evaluate factoextra FactoMineR fansi farver fastmap flashClust flexclust FNN fontawesome foreach 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 magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr modeltools multcompView munsell mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pixmap pkgconfig plyr polynom promises proxy purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppParallel RcppProgress RcppThread reshape2 rlang rmarkdown RSpectra rstatix rTensor Rtsne sass scales scatterplot3d shiny shinyjs sitmo sourcetools sp SparseM stringi stringr survival tibble tidyr tidyselect tinytex usedist utf8 uwot vctrs viridis viridisLite withr xfun xtable yaml

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

Kentaro Yamamoto, Koki Tsuyuzaki, Itoshi Nikaido

Rendered fromWormTensor.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2022-09-08
Started: 2022-09-08

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 0.1.1

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

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)