R Observatory: Metrics for tidyestimate version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tidyestimate

1.1.1

A Tidy Implementation of 'ESTIMATE'

0packages depend

4.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kai AragakiFirst published 2021-06-213 releasesCRAN page ↗GitHub ↗

The 'ESTIMATE' package infers tumor purity from expression data as a function of immune and stromal infiltrate, but requires writing of intermediate files, is un-pipeable, and performs poorly when presented with modern datasets with current gene symbols. 'tidyestimate' a fast, tidy, modern reimagination of 'ESTIMATE' (2013) doi:10.1038/ncomms3612.

Install

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

install.packages("tidyestimate", 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("KaiAragaki/tidyestimate")

Development version from KaiAragaki/tidyestimate. 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-tidyestimate

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-tidyestimate

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-tidyestimate

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-04
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
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-07
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 291 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 13%

Downloads

4.2K

CRAN downloads in the past year

Rank #5,849 · ~12/day · ~354/mo

Releases R versions

Daily download trend is not available in this view yet.

45630 days

1.4K90 days

4.2K1 year

Compare downloads with other packages →

Also on137 r2u24 autocran22 c2d4u

Repository

GitHub ↗ kaiaragaki/tidyestimate

19Stars

2Forks

0Open issues

0Open PRs

2Releases

168Commits

3Contributors

tidycancer-genomics

License GPL-2.0 · 168 commits · Last activity 2023-08-22 · 0% stars, 30d

Stars over time

2025-07-07 · 162026-07-07 · 19

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/kaiaragaki/tidyestimate on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (6)

glue dplyrstatsrlang ggrepel ggplot2

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Kai Aragaki

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Copyright holders (1)

Paul Roebuck

Copyright holder

Package Timeline

3 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
1.1.1Latest
2023-08-21 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1.0
2021-09-09 · diff ↗
1.0.4
2021-06-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-21
Total releases: 3 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 704 KB / 4 files
Download size: 915 KB
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("tidyestimate")

Format

Aragaki, K., Kim, H., Roebuck, P., Vegesna, R., Verhaak, R., & Yoshihara, K. (2023). tidyestimate: A Tidy Implementation of 'ESTIMATE' (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.tidyestimate

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 tidyestimate version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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