R Observatory: Metrics for scBSP version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scBSP

1.1.0

A Fast Tool for Single-Cell Spatially Variable Genes Identifications on Large-Scale Data

0packages depend

2.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jinpu LiFirst published 2024-02-093 releasesCRAN page ↗

Identifying spatially variable genes is critical in linking molecular cell functions with tissue phenotypes. This package utilizes a granularity-based dimension-agnostic tool, single-cell big-small patch (scBSP), implementing sparse matrix operation and KD tree methods for distance calculation, for the identification of spatially variable genes on large-scale data. The detailed description of this method is available at Wang, J. and Li, J. et al. 2023 (Wang, J. and Li, J. (2023), doi:10.1038/s41467-023-43256-5).

Install

R (CRAN)Ubuntu (r2u)

install.packages("scBSP", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-scbsp

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 57 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 94 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #19,528 · ~6/day · ~184/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

58290 days

2.2K1 year

Compare downloads with other packages →

Also on117 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

MatrixsparseMatrixStats fitdistrplus RANN spam

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Jinpu Li

Author, Maintainer

Authors (2)

Jinpu Li

Author, Maintainer

Yiqing Wang

Author · added in 1.0.0

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2025-09-01 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-05-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.0.1
2024-02-09
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-09
Total releases: 3 / 2 yrs
License: GPL (>= 2) OSI
Download size: 85 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scBSP")

Format

Li, J., & Wang, Y. (2025). scBSP: A Fast Tool for Single-Cell Spatially Variable Genes Identifications on Large-Scale Data (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.scBSP

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for scBSP version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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