rliger2.2.1 package

Align factor loadings to get final integration

Converting other classes of data to a liger object

Converting other classes of data to a ligerDataset object

Calculate agreement metric after integration

Calculate alignment metric after integration

Calculate adjusted Rand index (ARI) by comparing two cluster labeling ...

Calculate a dataset-specificity score for each factor

Calculate Normalized Mutual Information (NMI) by comparing two cluster...

Calculate purity by comparing two cluster labeling variables

Align factor loading by centroid alignment (beta)

Close all links (to HDF5 files) of a liger object

Check difference of two liger command

Convert old liger object to latest version

Access ligerSpatialDataset coordinate data

Create on-disk ligerDataset Object

Create liger object

Create in-memory ligerDataset object

Generate dot plot from input matrix with ComplexHeatmap

Produce single violin plot with data frame passed from upstream

Generic ggplot theme setting for rliger package

Produce single scatter plot with data frame passed from upstream

General heatmap plotting with prepared matrix and data.frames

Downsample datasets

Export predicted gene-pair interaction

Find shared and dataset-specific markers

Calculate proportion mitochondrial contribution

Apply function to chunks of H5 data in ligerDataset object

Import prepared dataset publically available

Impute the peak counts from gene expression data referring to an ATAC ...

Check if given liger object if under new implementation

Check if a liger or ligerDataset object is made of HDF5 file

liger class

Find DEG between groups

Subclass of ligerDataset for ATAC modality

ligerCommand object: Record the input and time of a LIGER function cal...

ligerDataset class

Subclass of ligerDataset for Methylation modality

Subclass of ligerDataset for RNA modality

Subclass of ligerDataset for Spatial modality

Convert between liger and Seurat 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

Create new variable from categories in cellMeta

Merge hdf5 files

Merge matrices while keeping the union of rows

Return preset modality of a ligerDataset object or that of all dataset...

Normalize raw counts data

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

Access ligerATACDataset peak data

Create barcode-rank plot for each dataset

Generate violin/box plot(s) using liger object

Make dot plot of factor loading in cell groups

Make dot plot of gene expression in cell groups

Create violin plot for multiple genes grouped by clusters

Create density plot basing on specified coordinates

Generate scatter plot(s) using liger object

Create volcano plot with EnhancedVolcano

Visualize factor expression and gene loading

Visualize GO enrichment test result in dot plot

Comprehensive group splited cluster plot on dimension reduction with p...

Plot Heatmap of Gene Expression or Factor Loading

Create heatmap for showing top marker expression in conditions

Create heatmap for pairwise DEG analysis result

Visualize proportion across two categorical variables

Box plot of cluster proportion in each dataset, grouped by condition

Make Riverplot/Sankey diagram that shows label mapping across datasets

Visualize a spatial dataset

Plot the variance vs mean of feature expression

Visualize gene expression or cell metadata with violin plot

Create volcano plot for Wilcoxon test result

Quantile align (normalize) factor loading

Quantile align (normalize) factor loadings

Quantile Align (Normalize) Factor Loadings

Load in data from 10X

Read 10X cellranger files (matrix, barcodes and features) into R sessi...

Read 10X HDF5 file

Read matrix from H5AD file

Read liger object from RDS file

See downsample

Objects exported from other packages

Remove missing cells or features from liger object

Restore links (to HDF5 files) for reloaded liger/ligerDataset object

Retrieve a single matrix of cells from a slot

Create "scaled data" for DNA methylation datasets

Deprecated functions in package rliger.

rliger: Linked Inference of Genomic Experimental Relationships

Perform consensus iNMF on scaled datasets

SNN Graph Based Community Detection

General QC for liger object

Run Gene Ontology enrichment analysis on differentially expressed gene...

Analyze biological interpretations of metagene

Perform iNMF on scaled datasets

Integrate scaled datasets with iNMF or variant methods

Perform online iNMF on scaled datasets

Perform t-SNE dimensionality reduction

Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features

Perform UMAP Dimensionality Reduction

Scale genes by root-mean-square across cells

Batch-aware highly variable gene selection

Select a subset of informative genes

Select variable genes from one dataset with Seurat VST method

Subset liger with brackets

Subset ligerDataset object

Get cell metadata variable

Subset liger object

Subset ligerDataset object

Suggest optimal K value for the factorization

Update old liger object to up-to-date structure

Write in-memory data into H5 file

Write liger object to H5AD files