PRECAST

1.9

Embedding and Clustering with Alignment for Spatial Omics Datasets

2packages depend

6.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Wei LiuFirst published 2022-06-2215 releasesCRAN page ↗GitHub ↗

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.

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

Health

CRAN checks

13OK

Slowest check: 18.5 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-05
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 899 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 96%
References docs: 16%

Downloads

6.4K

CRAN downloads in the past year

Rank #6,520 · ~18/day · ~536/mo

Releases R versions

Daily download trend is not available in this view yet.

54230 days

1.5K90 days

6.4K1 year

Compare downloads with other packages →

Also on476 r2u

Repository

GitHub ↗ feiyoung/precast

15Stars

3Forks

11Open issues

0Open PRs

1Releases

65Commits

2Contributors

License GPL-3.0 · 65 commits · Last activity 2025-12-15 · 0% stars, 30d

Stars over time

2024-12-18 · 102026-07-07 · 15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/feiyoung/precast on 2026-07-19.

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

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

2direct

0indirect

ProFAST coFAST

Code & Tests

Code Composition

R 2,962 (43%)C++ 1,573 (23%)Rd 1,143 (16%)Vignettes 1,093 (16%)C 174 (3%)

Code characteristics

Object systems

S32S4 class1S4 method1

Cyclomatic complexity: 2.0 median / 30 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

109 28 exported

Complexity

4.5 avg / 30 max

Call network

109 nodes / 79 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
Human_HK_genes	data.frame	2,833 × 4	in 2 packages
Mouse_HK_genes	data.frame	3,984 × 5	in 2 packages

People & History

People (3)

Maintainer (1)

Wei Liu

Author, Maintainer

Authors (3)

Wei Liu

Author, Maintainer

Jin Liu

Author

Yi Yang

Author

Package Timeline

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

1.9Latest
2026-06-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.8
2025-12-15 · diff ↗
1.7
2025-10-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.6
2025-03-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.5
2024-03-19 · diff ↗
1.6.4
2024-01-25 · diff ↗
1.6.3
2023-11-06 · diff ↗
1.6.2
2023-08-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6
2023-04-18 · diff ↗
1.5
2023-03-23 · diff ↗
1.4
2023-02-11 · diff ↗
1.3
2022-10-18 · diff ↗

Show 4 earlier events

1.2
2022-07-12 · diff ↗
1.1
2022-06-29 · diff ↗
1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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