Package: lstar 0.1.0

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_0.1.0.tar.gz
lstar_0.1.0.tar.gz(r-4.7-arm64)lstar_0.1.0.tar.gz(r-4.7-x86_64)lstar_0.1.0.tar.gz(r-4.6-arm64)lstar_0.1.0.tar.gz(r-4.6-x86_64)
lstar_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
lstar/json (API)
NEWS

# Install 'lstar' in R:

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

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

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

zlib cpp openmp

2.72 score 53 scripts 19 exports 3 dependencies

Last updated from:360ba1c499. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	510
linux-devel-x86_64	OK	536
source / vignettes	OK	631
linux-release-arm64	OK	545
linux-release-x86_64	OK	523
wasm-release	OK	198

Exports:col_sum_by_group collection_from field_value lstar_markers lstar_read lstar_read_block lstar_read_genes lstar_stream_col_sum_by_group lstar_write read_conos read_sce read_sce_backed read_seurat read_seurat_backed stream_col_stats write_conos write_pagoda2 write_sce write_seurat

Dependencies:cpp11 lattice Matrix

Converting between single-cell formats with lstar

Rendered fromconverting-formats.Rmdusingknitr::rmarkdownon Jun 22 2026.

Last update: 2026-06-22
Started: 2026-06-22

Citation

Readme and manuals

Help Manual

Help page	Topics
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
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
Print an L* dataset	print.lstar_dataset
Reconstruct a Conos object from an L* collection	read_conos
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
Build an L* dataset from a Conos object (a collection of samples).	write_conos
Export a Pagoda2 object to an L* (*.lstar.zarr) store.	write_pagoda2
Build a SingleCellExperiment from an L* dataset.	write_sce
Build a Seurat object from an L* dataset.	write_seurat