rliger

Calculate adjusted Rand index

Calculate agreement metric

Calculate alignment metric

Calculate alignment for each cluster

Calculate a dataset-specificity score for each factor

Calculate variance of gene expression across cells in an online fashion

Calculate purity

Convert older liger object into most current version (based on class definition)

Create a liger object.

Find shared and dataset-specific markers

Get gene expression values from list of expression matrices.

Calculate proportion mitochondrial contribution

Impute the query cell expression matrix

The LIGER Class

Create a Seurat object containing the data from a liger object

Linking genes to putative regulatory elements

Louvain algorithm for community detection

Fast calculation of feature count matrix

Export predicted gene-pair interaction

Generate a river (Sankey) plot

Merge hdf5 files

nnzeroGroups

Perform thresholding on dense matrix

Normalize raw datasets to column sums

Perform online iNMF on scaled datasets

Perform iNMF on scaled datasets

Perform factorization for new data

Perform factorization for new value of k

Perform factorization for new lambda value

Perform factorization for subset of data

Plot t-SNE coordinates of cells across datasets

Plot heatmap of cluster/factor correspondence

Plot cluster proportions by dataset

Plot scatter plots of unaligned and aligned factor loadings

Plot specific feature on t-SNE coordinates

Plot gene expression on dimensional reduction (t-SNE) coordinates

Generate t-SNE plots and gene loading plots

Plot violin plots for gene expression

Plot expression of multiple genes

Generate word clouds and t-SNE plots

Quantile align (normalize) factor loadings

Quantile align (normalize) factor loadings

rank_matrix

Read 10X alignment data (including V3)

Sample data for plotting

Remove cells/genes with no expression across any genes/cells

Construct a liger object organized by another feature

Restore links (to hdf5 files) for reloaded online Liger object

Analyze biological interpretations of metagene

Perform t-SNE dimensionality reduction

Perform UMAP dimensionality reduction

Perform Wilcoxon rank-sum test

Scale genes by root-mean-square across cells

Select a subset of informative genes

Create liger object from one or more Seurat objects

show method for liger

Construct a liger object with a specified subset

Visually suggest appropiate k value

Visually suggest appropriate lambda value

sumGroups