R Observatory: Metrics for gateR version 0.1.16

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gateR

0.1.16

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

0packages depend

3.1Kdownloads / year

74.4%test coverage

13/13checks pass

Overview

About

Maintained by Ian D. BullerFirst published 2020-11-1013 releasesCRAN page ↗GitHub ↗

Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) doi:10.1002/sim.7577. Details about kernel density estimation can be found in J. F. Bithell (1990) doi:10.1002/sim.4780090616. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) doi:10.1002/sim.4780101112.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("gateR", 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("lance-waller-lab/gateR")

Development version from lance-waller-lab/gateR. 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-gater

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-gateR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-gateR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.4 min · r-patched-linux-x86_64

Code health

Yes

Tests · ratio 0.25

74.4%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 644 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,918 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

79590 days

3.1K1 year

Compare downloads with other packages →

Also on93 r2u26 autocran

Repository

GitHub ↗ lance-waller-lab/gater

2Stars

3Forks

0Open issues

0Open PRs

13Releases

72Commits

5Contributors

rrstatscrancran-rcytometryflow-cytometrygatingkernel-density-estimation

License Apache-2.0 · 72 commits · Last activity 2025-09-10

Stars over time

2023-02-01 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/lance-waller-lab/gater on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practices

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (11)

fieldsgraphicsgrDeviceslifecycle rlang sparr SpatialPack spatstat.geomstatsterra tibble

LinkingTo (0)

none

Suggests (6)

dplyr R.rsp spelling testthat usethisutils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Ian D. Buller

Author, Maintainer, Copyright holder

Authors (1)

Ian D. Buller

Author, Maintainer, Copyright holder

Contributors (3)

Debashis Ghosh

Contributor

Elena Hsieh

Contributor

Lance A. Waller

Contributor

Copyright holders (2)

Ian D. Buller

Author, Maintainer, Copyright holder

NCI

Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.16Latest
2025-08-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.15
2024-01-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.13
2023-02-02 · diff ↗
0.1.12
2022-12-01 · diff ↗
0.1.11
2022-08-27 · diff ↗
unarchivedReturned to CRAN
2022-08-27
archivedRemoved from CRAN
2022-08-08
requires archived package 'SpatialPack'
R
R 4.2.0 released · 2022-04-22
0.1.10
2022-02-05 · diff ↗
0.1.9
2021-06-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.8
2021-03-15 · diff ↗

Show 6 earlier events

0.1.7
2021-02-04 · diff ↗
0.1.6
2021-01-07 · diff ↗
0.1.4
2020-11-30 · diff ↗
0.1.3
2020-11-17 · diff ↗
0.1.2
2020-11-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-10
Total releases: 13 / 6 yrs
License: Apache License (>= 2.0)
Minimum R: ≥ 3.5.0
Bundled data: 553 KB / 1 file
Download size: 860 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gateR")

Format

Buller, I. D., NCI, Ghosh, D., Hsieh, E., & Waller, L. A. (2025). gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation (Version 0.1.16) [Computer software]. https://doi.org/10.32614/CRAN.package.gateR

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 gateR version 0.1.16 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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