scMappR

1.0.12

Single Cell Mapper

0packages depend

3.9Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Dustin SokolowskiFirst published 2020-03-0413 releasesCRAN 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.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-linux-x86_64

Slowest check: 17.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.03

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-07-19
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 7 earlier snapshots

OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,381 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 38%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #10,809 · ~11/day · ~325/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

97090 days

3.9K1 year

Compare downloads with other packages →

Also on94 r2u

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Dustin Sokolowski

Author, Maintainer

Authors (9)

Dustin Sokolowski

Author, Maintainer

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

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

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

Show 9 earlier events

1.0.1
2021-03-30 · diff ↗
1.0.0
2021-03-22 · diff ↗
0.1.5
2020-11-30 · diff ↗
0.1.4
2020-09-02 · diff ↗
0.1.3
2020-07-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.1
2020-03-06 · diff ↗
0.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

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