R Observatory: Metrics for scBSP version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scBSP

1.1.0Package record

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

0packages depend

2.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jinpu LiCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 56 s · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 94 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%3 run in a plain check
Exported functions with examples: 75%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #19,882 · ~6/day · ~184/mo

Releases R versions

Daily download trend is not available in this view yet.

21830 days

67090 days

2.2K1 year

Compare downloads with other packages →

Also on70 r2u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing scBSP adds 6 packages (5 with compiled code, 8.1 MB of source tarballs). Heaviest: spam 3.1 MB, fitdistrplus 2.4 MB, Rcpp 1.8 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

People & History

People (2)

Jinpu Li

Author, Maintainer since 0.0.1 (2024)

Yiqing Wang

Author · added in 1.0.0

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-09-01 · current release · diff ↗ ·
added 1 export
CombinePvalues
R
R 4.5.0 released · 2025-04-11
1.0.0
record
2024-05-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.0.1
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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