Package: markerpen 0.1.2

markerpen: Marker Gene Detection via Penalized Principal Component Analysis

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.

Authors:Yixuan Qiu [aut, cre], Jiebiao Wang [aut], Jing Lei [aut], Kathryn Roeder [aut]

markerpen_0.1.2.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
markerpen/json (API)

# Install 'markerpen' in R:

install.packages('markerpen', repos = c('https://yixuan.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yixuan/markerpen/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

gene_mapping - Mapping gene names to Ensembl IDs

On CRAN:

openblas cpp openmp

4.48 score 6 stars 4 scripts 205 downloads 3 exports 5 dependencies

Last updated from:b521abf5ef. Checks:12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	163
linux-devel-x86_64	OK	150
source / vignettes	OK	245
linux-release-arm64	OK	139
linux-release-x86_64	OK	148
macos-release-arm64	OK	126
macos-release-x86_64	OK	429
macos-oldrel-arm64	OK	104
macos-oldrel-x86_64	OK	332
windows-devel	OK	153
windows-release	OK	195
windows-oldrel	OK	213
wasm-release	FAIL	119

Exports:pca_pen refine_markers sort_markers

Dependencies:lattice Matrix Rcpp RcppEigen RSpectra

MarkerPen: Marker Gene Detection via Penalized Principal Component Analysis

Introduction | Installation | Example

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2025-12-14
Started: 2021-02-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mapping gene names to Ensembl IDs	gene_mapping
Penalized Principal Component Analysis for Marker Gene Selection	pca_pen
Marker Gene Selection via Penalized Principal Component Analysis	refine_markers
Post-processing Selected Marker Genes	sort_markers