R Observatory: Metrics for RPPASPACE version 1.0.10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RPPASPACE

1.0.10

Reverse-Phase Protein Array Super Position and Concentration Evaluation

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by James M. MelottFirst published 2020-12-104 releasesCRAN page ↗GitHub ↗

Provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as 'tissue lysate arrays' or simply 'lysate arrays'. The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package named SuperCurve. For a detailed description of data inputs and outputs, usage information, and a list of related papers describing methods used in the package please review the vignette 'Guide_to_RPPASPACE'. 'RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data'. Bioinformatics Nov 15;38(22):5131-5133. <doi: 10.1093/bioinformatics/btac665>.

Install

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

install.packages("RPPASPACE", 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("MD-Anderson-Bioinformatics/rppaspace")

Development version from MD-Anderson-Bioinformatics/rppaspace. 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-rppaspace

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-RPPASPACE

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

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 3.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

22

Dependencies · direct

Check history

NOTE2026-04-25
10 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 97%
Return-value docs: 100%
References docs: 7%

Downloads

2.4K

CRAN downloads in the past year

Rank #15,096 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

69290 days

2.4K1 year

Compare downloads with other packages →

Also on126 r2u

Repository

GitHub ↗ md-anderson-bioinformatics/rppaspace

3Stars

1Forks

4Open issues

0Open PRs

2Releases

18Commits

1Contributors

18 commits · Last activity 2024-06-20

Stars over time

2025-03-21 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

Checks run against github.com/md-anderson-bioinformatics/rppaspace on 2026-08-09.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (6)

R >= 3.5.0methodsdoParallel foreachparalleliterators

Imports (17)

utilsgrDevicesgraphicsstatsbmp jpeg tiff png imager cobssplinesnlmerobustbasemgcvSparseM quantreg timeDate

LinkingTo (0)

none

Suggests (3)

bootknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (18)

Maintainer (1)

James M. Melott

Author, Maintainer

Authors (11)

James M. Melott

Author, Maintainer

Rehan Akbani

Author · added in 1.0.10

Keith A. Baggerly

Author · added in 1.0.10

Author

Author

Author

Author · added in 1.0.10

Shwetha V. Kumar

Author · added in 1.0.10

E. Shannon Neeley

Author · added in 1.0.10

Paul L. Roebuck

Author · added in 1.0.10

Huma Shehwana

Author · added in 1.0.10

Contributors (7)

Bradley M. Broom

Contributor · added in 1.0.10

Yiling Lu

Contributor · added in 1.0.10

Gordon B. Mills

Contributor · added in 1.0.10

Mary A. Rohrdanz

Contributor · added in 1.0.10

Doris R. Siwak

Contributor · added in 1.0.10

Chris Wakefield

Contributor · added in 1.0.10

John N. Weinstein

Contributor · added in 1.0.10

Listed in earlier versions (3)

Keith Baggerly

no longer listed · 1.0.7 to 1.0.9

Shannon Neeley

no longer listed · 1.0.7 to 1.0.9

Paul Roebuck

no longer listed · 1.0.7 to 1.0.9

Package Timeline

4 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
1.0.10Latest
2023-10-19 · current release · diff ↗
1.0.9
2023-08-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.8
2021-10-20 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.7
2020-12-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-10
Total releases: 4 / 6 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 3.5.0
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RPPASPACE")

Format

Melott, J. M., Akbani, R., Baggerly, K. A., Broom, B. M., Coombes, K. R., Hu, J., Joy, C., Ju, Z., Kumar, S. V., Lu, Y., Mills, G. B., Neeley, E. S., Roebuck, P. L., Rohrdanz, M. A., Shehwana, H., Siwak, D. R., Wakefield, C., & Weinstein, J. N. (2023). RPPASPACE: Reverse-Phase Protein Array Super Position and Concentration Evaluation (Version 1.0.10) [Computer software]. https://doi.org/10.32614/CRAN.package.RPPASPACE

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 RPPASPACE version 1.0.10 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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