R Observatory: Metrics for scMappR version 1.0.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scMappR

1.0.12Package record

Single Cell Mapper

0packages depend

3.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Dustin SokolowskiCRAN page ↗

The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. doi:10.1093/nargab/lqab011.

Install

R (CRAN)Ubuntu (r2u)

install.packages("scMappR", 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-scmappr

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-patched-linux-x86_64

Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

Additional issues

donttest

CRAN check page ↗

Slowest check: 13.8 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERROR2026-10-15
WARNING12 OK, 1 WARNING2026-09-25
OK13 OK2026-09-24
ERROR12 OK, 1 ERROR2026-09-17
OK13 OK2026-08-04

Show 14 earlier changesHide 14 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-26
ERROR12 OK, 1 ERROR2026-07-19
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-04-30
ERROR12 OK, 2 ERROR2026-04-09
OK14 OK2026-03-16
ERROR13 OK, 1 ERROR2026-03-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.12

READMEYes · 1,381 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 34
Examples that run: 38%13 run in a plain check · 21 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

single cell Mapper (scMappR)

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #8,965 · ~11/day · ~324/mo

Releases R versions

Daily download trend is not available in this view yet.

38630 days

1.1K90 days

3.9K1 year

Compare downloads with other packages →

Also on80 r2u

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing scMappR adds 165 packages (94 with compiled code, 143 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 3 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (16)

ggplot2 pheatmapgraphicsSeurat GSVAstatsutilsdownloader pcaMethodsgrDevicesgProfileR limSolve gprofiler2 pbapply ADAPTS reshape

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

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 (9)

Dustin Sokolowski

Author, Maintainer since 0.1 (2020)

Cadia Chan

Author · added in 0.1.4

Lauren Erdman

Author · added in 0.1.4

Mariela Faykoo-Martinez

Author

Anna Goldenberg

Author

Melissa Holmes

Author · added in 0.1.4

Houyun Hou

Author · added in 0.1.4

Michael Wilson

Author

Helen Zhu

Author · added in 0.1.4

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-06-25
1.0.12Latest
record
2025-06-25 · current release · diff ↗
archivedRemoved from CRAN
2025-06-02
requires archived package 'limSolve'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.11
record
2023-06-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2023-02-18
1.0.10
record
2023-02-18 · diff ↗
archivedRemoved from CRAN
2022-12-21
email to the maintainer was undeliverable
R
R 4.2.0 released · 2022-04-22
1.0.9
record
2022-03-07 · diff ↗
1.0.7
record
2021-10-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.2
record
2021-05-15 · diff ↗

Show 9 earlier eventsHide 9 earlier events

1.0.1
record
2021-03-30 · diff ↗
1.0.0
record
2021-03-22 · diff ↗
0.1.5
record
2020-11-30 · diff ↗ ·
added 2 exports
compare_deconvolution_methods, cwFoldChange_evaluate
0.1.4
record
2020-09-02 · diff ↗ ·
added 1 export
get_signature_matrices
0.1.3
record
2020-07-21 · diff ↗ ·
added 1 export
two_method_pathway_enrichment
R
R 4.0.0 released · 2020-04-24
0.1.1
record
2020-03-06 · diff ↗
0.1
record
2020-03-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-04
Total releases: 13 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 529 KB / 5 files
Download size: 651 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scMappR")

Format

Sokolowski, D., Chan, C., Erdman, L., Faykoo-Martinez, M., Goldenberg, A., Holmes, M., Hou, H., Wilson, M., & Zhu, H. (2025). scMappR: Single Cell Mapper (Version 1.0.12) [Computer software]. https://doi.org/10.32614/CRAN.package.scMappR

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 scMappR version 1.0.12 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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