This package is considered a duplicate. The official version of this package is found at:https://zhiyuan-hu-lab.r-universe.dev/CIDER

Package: CIDER 0.99.4

Zhiyuan Hu

CIDER: Meta-Clustering for scRNA-Seq Integration and Evaluation

A workflow of (a) meta-clustering based on inter-group similarity measures and (b) a ground-truth-free test metric to assess the biological correctness of integration in real datasets. See Hu Z, Ahmed A, Yau C (2021) <doi:10.1101/2021.03.29.437525> for more details.

Authors:Zhiyuan Hu [aut, cre], Christopher Yau [aut], Ahmed Ahmed [aut]

CIDER_0.99.4.tar.gz
CIDER_0.99.4.tar.gz(r-4.5-noble)CIDER_0.99.4.tar.gz(r-4.4-noble)
CIDER_0.99.4.tgz(r-4.4-emscripten)
CIDER.pdf |CIDER.html✨
CIDER/json (API)
NEWS

# Install 'CIDER' in R:

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

Bug tracker:https://github.com/zhiyuan-hu-lab/cider/issues

Pkgdown site:https://zhiyuan-hu-lab.github.io

Datasets:

pancreas_meta - Pancreas Metadata

On CRAN:

4.00 score 415 downloads 18 mentions 14 exports 157 dependencies

Last updated 1 months agofrom:8bcd5a344c. Checks:3 OK. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 09 2025
R-4.5-linux	OK	Mar 09 2025
R-4.4-linux	OK	Mar 09 2025

Exports:calculateDistMatOneModel downsampling estimateProb finalClustering gatherInitialClusters getDistMat getIDEr hdbscan.seurat initialClustering mergeInitialClusters plotDistMat plotHeatmap plotNetwork scatterPlot

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table dbscan deldir digest doParallel dotCall64 dplyr dqrng edgeR evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband iterators jquerylib jsonlite kernlab KernSmooth knitr labeling later lattice lazyeval leidenbase lifecycle limma listenv lmtest locfit magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridis viridisLite withr xfun xtable yaml zoo

Evaluating scRNA-seq Integration Quality with CIDER

Rendered fromevaluation.Rmdusingknitr::rmarkdownon Mar 09 2025.

Last update: 2025-02-07
Started: 2025-02-07

Getting Start with Assisted CIDER (asCIDER)

Rendered fromasCIDER.Rmdusingknitr::rmarkdownon Mar 09 2025.

Last update: 2025-02-07
Started: 2025-02-07

Citation

Readme and manuals

Help Manual

Help page	Topics
Calculate Distance Matrix Using a Single Model	calculateDistMatOneModel
Downsampling Cells	downsampling
Estimate the Empirical Probability of Whether Two Set of Cells from Distinct Batches Belong to the Same Population	estimateProb
Final Clustering Step for Meta-Clustering	finalClustering
Gather Initial Cluster Names	gatherInitialClusters
Calculate the Similarity Matrix	getDistMat
Calculate IDER-Based Similarity Between Two Groups	getGroupFit
Compute IDER-Based Similarity	getIDEr
Initial Clustering for Evaluating Integration	hdbscan.seurat
Initial Clustering	initialClustering
Merge Initial Clusters	mergeInitialClusters
Pancreas Metadata	pancreas_meta
Plot Similarity Matrix with pheatmap	plotDistMat
Plot Heatmap for the IDER-Based Similarity Matrix	plotHeatmap
Plot Network Graph	plotNetwork
Scatterplot by a selected feature	scatterPlot