CEB package

CEB depends on multiple packages, including mclust, fpc, vegan, apcluster, factoextra, ADPclust, SC3, SingleCellExperiment, Rtsne, kernlab. To make sure all the dependency packages are installed.

Download CEB_0.1.1.tar.gz Install R package locally from R studio.

Data Input

Data input provides the interface for users to upload data for the construction of CEB.

RNA data

The expression profiles of single-cell RNA data. The rows of uploaded files should represent RNA, while the columns should represent samples.

Methylation data

The expression profiles of single-cell DNA methylation data. The rows of uploaded files should represent DNA methylation rates (from 0 to 1) summarised at the feature level (i.e. promotes, gene bodies, etc.), while the columns should represent samples.

Just upload the data and parameters to get the result.

CEB_result <- CEB(dataset_list, feature.filter = T, feature.filter.fraction = 0.06, 
                  datatype = "count", log.trans = F,
                  SC3 = T, gene_filter = F, svm_num_cells = 5000, 
                  tSNE = T, dimensions = 3, perplexity = 30, tsne_min_cells = 200, 
                  tsne_min_perplexity = 10, var_genes = NULL,
                  kmeans = T, iter.max = 100,
                  spectral_cluster = T,
                  DBSCAN = F, eps = 270, MinPts = 5,
                  hierarchical_clustering = F, distance_form = "euclidean",
                  SEED = 1)