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:
CIDER_0.99.4.tar.gz
CIDER_0.99.4.zip(r-4.5)CIDER_0.99.4.zip(r-4.4)CIDER_0.99.4.zip(r-4.3)
CIDER_0.99.4.tgz(r-4.5-any)CIDER_0.99.4.tgz(r-4.4-any)CIDER_0.99.4.tgz(r-4.3-any)
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://zhiyuan-hu-lab.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
- pancreas_meta - Pancreas Metadata
Last updated 1 months agofrom:071f146469. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 10 2025 |
| R-4.5-win | OK | Mar 10 2025 |
| R-4.5-mac | OK | Mar 10 2025 |
| R-4.5-linux | OK | Mar 10 2025 |
| R-4.4-win | OK | Mar 10 2025 |
| R-4.4-mac | OK | Mar 10 2025 |
| R-4.4-linux | OK | Mar 10 2025 |
| R-4.3-win | OK | Mar 10 2025 |
| R-4.3-mac | OK | Mar 10 2025 |
Exports:calculateDistMatOneModeldownsamplingestimateProbfinalClusteringgatherInitialClustersgetDistMatgetIDErhdbscan.seuratinitialClusteringmergeInitialClustersplotDistMatplotHeatmapplotNetworkscatterPlot
Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledbscandeldirdigestdoParalleldotCall64dplyrdqrngedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachfsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglaterlatticelazyevalleidenbaselifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisviridisLitewithrxfunxtableyamlzoo
Evaluating scRNA-seq Integration Quality with CIDER
Rendered fromevaluation.Rmdusingknitr::rmarkdownon Mar 10 2025.Last update: 2025-02-07
Started: 2025-01-31
Getting Start with Assisted CIDER (asCIDER)
Rendered fromasCIDER.Rmdusingknitr::rmarkdownon Mar 10 2025.Last update: 2025-02-07
Started: 2025-01-31
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 |
