R Observatory: Metrics for blisa version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

blisa

1.0.0Package record

Infer Cell-Cell Communication from Spatial Transcriptomics

0packages depend

1.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yunshun ChenCRAN page ↗GitHub ↗Website ↗Issues ↗

Identifies cell-cell communication hotspots in spatial transcriptomics data using bivariate Local Moran's I statistics on hexagonally binned cells. Provides functions for spatial weighting, ligand-receptor pair filtering, hotspot detection, and visualisation of sender-receiver cell-type interactions.

Changes in 1.0.0

blisa() now uses the fastLISA C/OpenMP backend by default (fast = TRUE) for the bivariate local Moran's I computation. fastLISA moved from Suggests to Imports. Results are statistically equivalent to the previous spdep::localmoran_bv backend but not bit-identical (different RNG).
New min_total_counts argument to blisa() and hexBinCells() drops bins whose total counts (summed over all genes) fall below the threshold during binning. Default 10.
New verbose argument (default FALSE) to blisa() and hexBinCells() gates progress messages; blisa() also shows a progress bar over the ligand-receptor pairs in interactive sessions.
New lr_pairs argument to plotCCI() selects specific ligand-receptor pairs to display, overriding top_lr.

Show all changes in 1.0.0Hide the rest of the changes in 1.0.0

New main argument to plotCCI(), plotCCILR(), and plotCCIsummary() adds a title above the heatmap.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ChenLaboratory/blisa")

Development version from ChenLaboratory/blisa. Installs pak first if it is not already available.

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-blisa

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: 3.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK7 OK2026-06-03

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 34 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.0.0Citation fileNoWebsiteYes · pkgdown

Help pages: 14 (1 internal)includes a package overview page
Examples that run: 8%1 run in a plain check · 11 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Exploring cell-cell interaction with blisa

How these are measured

Downloads

1.5K

CRAN downloads in the past year

Rank #11,909 · ~4/day · ~129/mo

Releases R versions

Daily download trend is not available in this view yet.

40330 days

90990 days

1.5K1 year

Compare downloads with other packages →

Also on30 r2u

How downloads are counted

Repository

chenlaboratory/blisa ↗Organization: ChenLaboratory

0Stars

0Forks

1Open issues

0Open PRs

0Releases

Last activity 2026-08-11 · Default branch at 1.0.2, ahead of CRAN 1.0.0 (checked 2026-10-11)

Responsiveness

not measured

Issues over time

2026-07-10 · 02026-09-18 · 1

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/chenlaboratory/blisa on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-08-11 · The repository has a site deploy workflow

pkgdown site last built 2026-08-11

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing blisa adds 31 packages (19 with compiled code, 43 MB of source tarballs). Heaviest: sf 9.3 MB, ggplot2 6.0 MB, spdep 4.5 MB. 3 more not on CRAN are not measured.

Depends (0)

none

Imports (10)

sf spdep fastLISAMatrixSpatialExperiment SummarizedExperiment ComplexHeatmap ggplot2 viridisLitegrid

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 (3)

Yunshun Chen

Author, Maintainer since 0.2.0 (2026)

Lizhong Chen

Author

Lei Qin

Author

Releases (2)

Pick two releases to compare their code metrics.

1.0.0Latest
record
2026-07-10 · current release · diff ↗
0.2.0
record
2026-06-02
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-02
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("blisa")

Format

Chen, Y., Chen, L., & Qin, L. (2026). blisa: Infer Cell-Cell Communication from Spatial Transcriptomics (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.blisa

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 blisa version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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