R Observatory: Metrics for markerpen version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

markerpen

0.1.2Package record

Marker Gene Detection via Penalized Principal Component Analysis

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yixuan QiuCRAN page ↗

Implementation of the 'MarkerPen' algorithm, short for marker gene detection via penalized principal component analysis, described in the paper by Qiu, Wang, Lei, and Roeder (2021, doi:10.1093/bioinformatics/btab257). 'MarkerPen' is a semi-supervised algorithm for detecting marker genes by combining prior marker information with bulk transcriptome data.

Changes in 0.1.2

NEW FEATURES

Updated the eigen solver code for future releases of RSpectra.

BUG FIXES

Removed the explicit requirement for C++11 in DESCRIPTION.
Updated the citation information.

From inst/NEWS.Rd in the release

Install

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

install.packages("markerpen", 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-markerpen

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-markerpen

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-markerpen

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 347 wordsVignettesYes · 1 · dynamicNEWSYes · mentions 0.1.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%2 run in a plain check
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (1)

MarkerPen: Marker Gene Detection via Penalized Principal Component Analysis

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #15,045 · ~8/day · ~242/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

79190 days

2.9K1 year

Compare downloads with other packages →

Also on420 r2u8 autocran81 c2d4u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing markerpen adds 3 packages (3 with compiled code, 3.6 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, RSpectra 125 KB.

Depends (1)

R >= 4.3.0

Imports (3)

Rcpp RSpectrastats

LinkingTo (3)

Rcpp RcppEigen RSpectra

Suggests (4)

knitr rmarkdown prettydoc scales

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Yixuan Qiu

Author, Maintainer since 0.1.0 (2021)

Jing Lei

Author

Kathryn Roeder

Author

Jiebiao Wang

Author

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
record
2025-12-14 · current release · diff ↗
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
0.1.1
record
2021-03-17 · diff ↗
0.1.0
record
2021-03-11
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-11
Total releases: 3 / 5 yrs
License: GPL
Minimum R: ≥ 4.3.0
Bundled data: 286 KB / 1 file
Download size: 3.5 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("markerpen")

Format

Qiu, Y., Lei, J., Roeder, K., & Wang, J. (2025). markerpen: Marker Gene Detection via Penalized Principal Component Analysis (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.markerpen

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 markerpen version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →