R Observatory: Metrics for phateR version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phateR

1.0.7

PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding

0packages depend

10.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Scott GiganteFirst published 2018-05-279 releasesCRAN page ↗

PHATE is a tool for visualizing high dimensional single-cell data with natural progressions or trajectories. PHATE uses a novel conceptual framework for learning and visualizing the manifold inherent to biological systems in which smooth transitions mark the progressions of cells from one state to another. To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic stem cells, human embryonic stem cells, and bone marrow samples, check out our publication in Nature Biotechnology at doi:10.1038/s41587-019-0336-3.

Install

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

install.packages("phateR", 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-phater

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-phateR

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-phateR

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

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
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 664 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 60%
References docs: 0%

Downloads

10.5K

CRAN downloads in the past year

Rank #5,200 · ~29/day · ~873/mo

Releases R versions

Daily download trend is not available in this view yet.

48530 days

1.5K90 days

10.5K1 year

Compare downloads with other packages →

Also on204 r2u15 autocran1.4K conda_forge22 c2d4u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.3Matrix

Imports (6)

methodsstatsgraphicsreticulate ggplot2 memoise

LinkingTo (0)

none

Suggests (2)

gridGraphics cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Scott Gigante

Maintainer

Authors (1)

Krishnan Srinivasan

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.7Latest
2021-02-12 · current release · diff ↗
1.0.4
2020-05-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.0
2019-12-05 · diff ↗
0.4.1
2019-04-26 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.4.0
2019-04-13 · diff ↗
0.2.9
2018-09-11 · diff ↗
0.2.8
2018-07-03 · diff ↗
0.2.7
2018-06-01 · diff ↗

Show 2 earlier events

0.2.6
2018-05-27
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-05-27
Total releases: 9 / 8 yrs
License: GPL-2 | file LICENSE OSI
Minimum R: ≥ 3.3
Bundled data: 2.3 MB / 2 files
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phateR")

Format

Gigante, S., & Srinivasan, K. (2021). phateR: PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.phateR

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 phateR version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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