Package: RepeatedHighDim 2.5.0

RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data

A toolkit for the analysis of high-dimensional repeated measurements, providing functions for outlier detection, differential expression analysis, gene-set tests, and binary random data generation.

Authors:Klaus Jung [aut, cre], Jochen Kruppa [aut], Sergej Ruff [aut]

RepeatedHighDim_2.5.0.tar.gz
RepeatedHighDim_2.5.0.zip(r-4.7)RepeatedHighDim_2.5.0.zip(r-4.6)RepeatedHighDim_2.5.0.zip(r-4.5)
RepeatedHighDim_2.5.0.tgz(r-4.6-any)RepeatedHighDim_2.5.0.tgz(r-4.5-any)
RepeatedHighDim_2.5.0.tar.gz(r-4.7-any)RepeatedHighDim_2.5.0.tar.gz(r-4.6-any)
RepeatedHighDim_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RepeatedHighDim/json (API)

# Install 'RepeatedHighDim' in R:

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

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 9 scripts 211 downloads 23 exports 200 dependencies

Last updated from:066a98712d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	357
source / vignettes	OK	374
linux-release-x86_64	OK	358
macos-release-arm64	OK	280
macos-oldrel-arm64	OK	212
windows-devel	OK	257
windows-release	OK	248
windows-oldrel	OK	266
wasm-release	OK	220

Exports:bag check_limma depmed fc_ci fc_plot GA_diagplot gem GlobTestMissing gridfun hldepth iter_matrix loop netRNA RHighDim rho_bounds rmvbinary_EP rmvbinary_QA scTC_bpplot scTC_trim_effect scTrimClust sequence_probs start_matrix summary_RHD

Dependencies:abind alphahull askpass base64enc BH BiocGenerics bit bit64 bitops boot bslib cachem caTools circlize class cli clipr clue cluster codetools colorspace commonmark ComplexHeatmap CompQuadForm cowplot cpp11 crayon crosstalk curl data.table ddalpha deldir DEoptimR digest doParallel dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics geometry GetoptLong ggplot2 ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr ica igraph interp IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle linprog listenv lme4 lmtest lpSolve magic magrittr MASS mathjaxr Matrix matrixStats memoise meta metabook metadat metafor mime miniUI minqa mvtnorm netmeta nlme nloptr numDeriv openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip prettyunits progress progressr promises purrr R.methodsS3 R.oo R.utils R6 RANN rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML Rdpack readr reformulas reshape2 reticulate rgl rjson rlang rmarkdown robustbase ROCR rprojroot RSpectra Rtsne S4Vectors S7 sass scales scattermore sctransform Seurat SeuratObject sfsmisc sgeostat shape shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils splancs stringi stringr survival sys tensor tibble tidyr tidyselect tinytex tzdb utf8 uwot vctrs viridisLite vroom withr xfun xml2 xtable yaml zoo

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Readme and manuals

Help Manual

Help page	Topics
Calculates the bag	bag
Calculates the depth median.	depmed
Calculation of adjusted confidence intervals	fc_ci
Volcano plot of adjusted confidence intervals	fc_plot
Diagnostic plot for comparison of two correlation matrices.	GA_diagplot
Plots a gemstone to an interactive graphics device	gem
Detection of global group effect	GlobTestMissing
Specifies grid for the calculation of the halfspace location depths	gridfun
Calculates the halfspace location depth	hldepth
Genetic algorithm for generating correlated binary data	iter_matrix
Calculates the fence and the loop	loop
netRNA:Network meta-analysis for gene expression data	netRNA
RepeatedHighDim Package	RepeatedHighDim-package RepeatedHighDim
Detection of global group effect	RHighDim
Calculate lower and upper the bounds for pairwise correlations	rho_bounds
Simulating correlated binary variables using the algorithm by Emrich and Piedmonte (1991)	rmvbinary_EP
Simulating correlated binary variables using the algorithm by Qaqish (2003)	rmvbinary_QA
scTC_bpplot: Post-trim breakpoint heatmap for scTrimClust results	scTC_bpplot
scTC_trim_effect: Compare scTrimClust trimming against default Seurat analysis	scTC_trim_effect
scTrimClust: Cluster visualization with alpha hull-based outlier detection	scTrimClust
ScTrimDist: Trim extreme cells based on kNN distance within cell types	scTrimDist
Calculation of probabilities for binary sequences	sequence_probs
Setup of the start matrix	start_matrix
Summary of RHighDim function	summary_RHD

Package: RepeatedHighDim 2.5.0

RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)