Package: lstar 0.2.1

Peter Kharchenko

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

A lightweight interchange layer for single-cell and spatial omics data, built on the L-star model of labelled axes and typed fields over them, serialized to the 'Zarr' format. Provides bidirectional converters ("profiles") for 'Seurat', 'SingleCellExperiment', 'Conos', and 'pagoda2' objects, including collections of heterogeneous samples, via a shared C++ core ('libstar') so the same store is readable from R, 'Python', and C++.

Authors:Peter Kharchenko [aut, cre]

lstar_0.2.1.tar.gz
lstar_0.2.1.zip(r-4.7)lstar_0.2.1.zip(r-4.6)lstar_0.2.1.zip(r-4.5)
lstar_0.2.1.tgz(r-4.6-x86_64)lstar_0.2.1.tgz(r-4.6-arm64)lstar_0.2.1.tgz(r-4.5-x86_64)lstar_0.2.1.tgz(r-4.5-arm64)
lstar_0.2.1.tar.gz(r-4.7-arm64)lstar_0.2.1.tar.gz(r-4.7-x86_64)lstar_0.2.1.tar.gz(r-4.6-arm64)lstar_0.2.1.tar.gz(r-4.6-x86_64)
lstar_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lstar/json (API)

# Install 'lstar' in R:

install.packages('lstar', repos = c('https://kharchenkolab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kharchenkolab/lstar/issues

Uses libs:

zlib– Compression library
libzstd– Fast lossless compression algorithm
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

zlib libzstd cpp openmp

5.64 score 2 stars 73 scripts 405 downloads 23 exports 3 dependencies

Last updated from:bb67ece66f. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	205
linux-devel-x86_64	OK	248
source / vignettes	OK	314
linux-release-arm64	OK	196
linux-release-x86_64	OK	263
macos-release-arm64	OK	126
macos-release-x86_64	OK	208
macos-oldrel-arm64	OK	146
macos-oldrel-x86_64	OK	259
windows-devel	OK	196
windows-release	OK	187
windows-oldrel	OK	164
wasm-release	OK	189

Exports:col_sum_by_group collection_from extend_for_viewer field_value lstar_markers lstar_read lstar_read_block lstar_read_genes lstar_stream_col_sum_by_group lstar_write lstar_write_viewer read_conos read_pagoda2 read_sce read_sce_backed read_seurat read_seurat_backed stream_col_stats view viewer_extend write_conos write_sce write_seurat

Dependencies:cpp11 lattice Matrix

Converting between single-cell formats with lstar

The model in R, end to end | Converting to and from Seurat / SingleCellExperiment | The lstar convert command line

Rendered fromconverting-formats.Rmdusingknitr::rmarkdown

Last update: 2026-06-14
Started: 2026-06-14

Citation

Development and contributors

Readme and manuals

Help Manual

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