R Observatory: Metrics for scITD version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before 2026-08-21 or it will be archived.

scITD

1.0.4

Single-Cell Interpretable Tensor Decomposition

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jonathan MitchelFirst published 2021-11-034 releasesCRAN page ↗

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) doi:10.1007/BF02289464. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) doi:10.1007/s13253-011-0055-9. Zhou, G., & Cichocki, A. (2012) doi:10.2478/v10175-012-0051-4.

Install

R (CRAN)Ubuntu (r2u)

install.packages("scITD", 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-scitd

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

13OK

Slowest check: 6.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

22

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 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

Show 6 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
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 · 300 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

2.9K

CRAN downloads in the past year

Rank #12,063 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

23630 days

82390 days

2.9K1 year

Compare downloads with other packages →

Also on378 r2u

Dependencies

Declared dependencies

38 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0.0Matrix

Imports (21)

rTensor ica fgsea circlize reshape2parallelComplexHeatmap ggplot2mgcvutilsRcpp RColorBrewer dplyr edgeR svastatsRmisc ggpubr msigdbr sccore NMF

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Suggests (20)

methodsknitr rmarkdown testthat coda.basegridsimplifyEnrichment WGCNA cowplot matrixStats stringr zoo rlang AnnotationDbi GO.db conos pagoda2 betareg slam tm

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Jonathan Mitchel

Maintainer, Author

Authors (3)

Jonathan Mitchel

Maintainer, Author

Evan Biederstedt

Author

Peter Kharchenko

Author

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
1.0.4Latest
2023-09-08 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.2
2022-03-23 · diff ↗
1.0.1
2022-01-29 · diff ↗
1.0.0
2021-11-03
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-03
Total releases: 4 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 13 KB / 1 file
Download size: 602 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scITD")

Format

Mitchel, J., Biederstedt, E., & Kharchenko, P. (2023). scITD: Single-Cell Interpretable Tensor Decomposition (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.scITD

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 scITD version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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