Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics

Documentation for package ‘lstar’ version 0.2.1

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.lstar_drop_cache	Build a Seurat object from an L* dataset.
collection_from	Assemble a collection of heterogeneous samples from per-sample objects.
col_sum_by_group	Per-(group, gene) sufficient stats over a CSC measure (the shared libstar kernel).
extend_for_viewer	Extend an L* dataset with the viewer@0.1 navigator fields (native R).
field_value	Accessor: a field's value by name.
lstar_markers	Tidy marker table for a factor's DE bundle.
lstar_read	Read an L* Zarr store into an R dataset.
lstar_read_block	Read a contiguous gene (column) range of a CSC measure from an L* store, bounded-memory.
lstar_read_genes	Read an arbitrary set of gene columns of a CSC measure, returning cells x genes.
lstar_stream_col_sum_by_group	Per-(group, gene) sums of a CSC measure in a store, streamed and bounded-memory.
lstar_write	Write an R dataset to an L* Zarr store.
lstar_write_viewer	Write an R dataset to an L* store, optionally extending it for the viewer first.
print.lstar_dataset	Print an L* dataset
read_conos	Reconstruct a Conos object from an L* collection
read_pagoda2	Read a Pagoda2 object into an L* dataset.
read_sce	Read a SingleCellExperiment into an L* dataset.
read_sce_backed	Open an .h5ad's expression matrix as a disk-backed SingleCellExperiment assay (via HDF5Array).
read_seurat	Read a Seurat object into an L* dataset.
read_seurat_backed	Open an .h5ad's expression matrix as a disk-backed Seurat v5 assay (via BPCells).
stream_col_stats	Per-gene mean/variance of a CSC measure in a store, read with bounded memory.
view	Open an object or L* store in the pagoda3 viewer (delegates to the 'pagoda3' package)
viewer_extend	Extend an existing L* store in place with the viewer@0.1 navigator fields.
write_conos	Build an L* dataset from a Conos object (a collection of samples).
write_sce	Build a SingleCellExperiment from an L* dataset.
write_seurat	Write an L* dataset to a Seurat object.