R Observatory: Metrics for PRECAST version 1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PRECAST

1.9Package record

Embedding and Clustering with Alignment for Spatial Omics Datasets

0packages dependsuggested by 2

6.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Wei LiuCRAN page ↗GitHub ↗Issues ↗

An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) doi:10.1038/s41467-023-35947-w.

Install

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

install.packages("PRECAST", 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("feiyoung/PRECAST")

Development version from feiyoung/PRECAST. 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-precast

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: 14.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-18
ERROR12 OK, 1 ERROR2026-10-11
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-12

Show 7 earlier changesHide 7 earlier changes

ERROR12 OK, 1 ERROR2026-07-05
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.9

READMEYes · 899 wordsVignettesYes · 5 · dynamicNEWSNoCitation fileNo

Help pages: 32
Examples that run: 88%15 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 65%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 16%

Vignettes (5)

PRECAST HTML
PRECAST: DLPFC Single Sample Analysis HTML
PRECAST: Four DLPFC Sample Analysis HTML
PRECAST: Human Breast Cancer Data Analysis HTML
PRECAST: simulation HTML

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #4,238 · ~18/day · ~550/mo

Releases R versions

Daily download trend is not available in this view yet.

97130 days

2.1K90 days

6.6K1 year

Compare downloads with other packages →

Also on454 r2u

How downloads are counted

Repository

feiyoung/precast ↗Account: feiyoung

17Stars

3Forks

11Open issues

0Open PRs

1Releases

65Commits

2Commit identities

License file reads as GPL-3.0 · 65 commits · Last activity 2025-12-15 · +6.3% stars, 30d · The default branch showed an older version (1.8) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-10-15 · 122026-10-02 · 17

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/feiyoung/precast on 2026-10-11.

Docs source (1)

GitHub Pages site last deployed 2025-12-15

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing PRECAST adds 169 packages (96 with compiled code, 162 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 2 more not on CRAN are not measured.

Depends (3)

R >= 4.0.0parallelgtools

Imports (22)

MASSMatrixmclustmethodspurrrutilsSeurat irlba cowplot patchwork scater pbapply ggthemes dplyr ggplot2statsDR.SC scales ggpubrgraphicscolorspace Rcpp (>= 1.0.5)

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

ProFAST coFAST

How these are counted

Code & Tests

Datasets

People & History

People (3)

Wei Liu

Author, Maintainer since 1.0 (2022)

Jin Liu

Author

Yi Yang

Author

Releases (15)

Pick two releases to compare their code metrics.

1.9Latest
record
2026-06-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.8
record
2025-12-15 · diff ↗
1.7
record
2025-10-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.6
record
2025-03-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.5
record
2024-03-19 · diff ↗
1.6.4
record
2024-01-25 · diff ↗
1.6.3
record
2023-11-06 · diff ↗
1.6.2
record
2023-08-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6
record
2023-04-18 · diff ↗ ·
removed 3 exports
selectModel, selectModel.PRECASTObj, selectModel.SeqK_PRECAST_Object

added 3 exports
SelectModel, SelectModel.PRECASTObj, SelectModel.SeqK_PRECAST_Object
1.5
record
2023-03-23 · diff ↗ ·
added 2 exports
drawFigs, chooseColors
1.4
record
2023-02-11 · diff ↗
1.3
record
2022-10-18 · diff ↗ ·
removed 1 export
gendata_seulist

Show 4 earlier eventsHide 4 earlier events

1.2
record
2022-07-12 · diff ↗
1.1
record
2022-06-29 · diff ↗ ·
removed 1 export
ridgePlot
1.0
record
2022-06-22
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-22
Total releases: 15 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.2 MB / 3 files
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PRECAST")

Format

Liu, W., Liu, J., & Yang, Y. (2026). PRECAST: Embedding and Clustering with Alignment for Spatial Omics Datasets (Version 1.9) [Computer software]. https://doi.org/10.32614/CRAN.package.PRECAST

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 PRECAST version 1.9 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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