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CIDER (version 0.99.1)

Meta-Clustering for Single-Cell Data Integration and Evaluation

Description

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) for more details.

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Install

install.packages('CIDER')

Monthly Downloads

86

Version

0.99.1

License

MIT + file LICENSE

Issues

3

Pull Requests

0

Stars

6

Forks

5

Maintainer

Zhiyuan Hu

Last Published

September 19th, 2022

Functions in CIDER (0.99.1)

measureSimilarity

Measure similarity between two vectors
initialClustering

Initial clustering
pancreas

Pancreatic scRNA-Seq data.
plotNetwork

Plot Network Graph
scatterPlot

Scatterplot by a selected feature
getIDEr

Compute IDER-based similarity
estimateProb

Estimate the empirical probability of whether two set of cells from distinct batches belong to the same population
getGroupFit

Calculate IDER-based similarity between two groups
downsampling

Downsampling cells
gatherInitialClusters

Gather initial cluster names
getDistMat

Calculate the Similarity Matrix
hdbscan.seurat

Initial clustering for evaluating integration
cosineSimilarityR

cosine similarity in R
finalClustering

Final clustering step for meta-clustering
calculateDistMatOneModel

Calculate distance matrix with in one model
plotDistMat

Plot Similarity Matrix with pheatmap
mergeInitialClusters

Merge Initial Clusters
plotHeatmap

Plot Heatmap for the IDER-based similarity matrix