R Observatory: Metrics for TCA version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TCA needs lambda.r (through futile.logger), which is past its CRAN deadline of Oct 12 to fix its check problems.

TCA

1.2.1Package record

Tensor Composition Analysis

0packages depend

3.9Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Elior RahmaniCRAN page ↗GitHub ↗Website ↗Issues ↗

Tensor Composition Analysis (TCA) allows the deconvolution of two-dimensional data (features by observations) coming from a mixture of heterogeneous sources into a three-dimensional matrix of signals (features by observations by sources). The TCA framework further allows to test the features in the data for different statistical relations with an outcome of interest while modeling source-specific effects; particularly, it allows to look for statistical relations between source-specific signals and an outcome. For example, TCA can deconvolve bulk tissue-level DNA methylation data (methylation sites by individuals) into a three-dimensional tensor of cell-type-specific methylation levels for each individual (i.e. methylation sites by individuals by cell types) and it allows to detect cell-type-specific statistical relations (associations) with phenotypes. For more details see Rahmani et al. (2019) DOI:10.1038/s41467-019-11052-9.

Changes in 1.2.1

*NOTE* v1.2.1 is not backward compatible with earlier versions

Changes:

A new argument 'vars.mle' in 'tca' which controls the method used for optimization; setting to FALSE allows a much faster optimization.
A new argument 'fast_mode' in 'tcareg' allows a much faster optimization.
A new argument 'constrain_mu' in 'tca' allows to determine whether to constrain the mean parameters in the optimization; setting to false now allows to obtain p-values for the covariates in 'C1' and 'C2'.
A new 'scale' argument in 'tensor' for dividing estimates by estimated standard deviations.
Default values of several arguments have been changed.
Switched the default FDR method used in ‘tcareg’ back from “BY” to “BH” (can be changed by editing the config file).

From NEWS.md in the release

Install

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

install.packages("TCA", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("cozygene/TCA")

Development version from cozygene/TCA. Installs pak first if it is not already available.

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-tca

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-TCA

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-TCA

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Elior Rahmani <elior.rahmani@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 588 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 1.2.1Citation fileYes · cites a publicationWebsiteYes

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 67%

Vignettes (1)

Detecting differential DNA methylation at cell-type resolution using TCA

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #7,873 · ~11/day · ~326/mo

Releases R versions

Daily download trend is not available in this view yet.

46430 days

1.1K90 days

3.9K1 year

Compare downloads with other packages →

Also on100 r2u9 autocran585 conda_forge55 c2d4u

How downloads are counted

Repository

cozygene/tca ↗Organization: cozygene

21Stars

11Forks

4Open issues

0Open PRs

2Releases

55Commits

3Commit identities

55 commits · Last activity 2021-02-14 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-01-31 · 182026-09-02 · 21

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/cozygene/tca on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing TCA adds 17 packages (6 with compiled code, 13 MB of source tarballs). Heaviest: data.table 5.7 MB, rsvd 3.3 MB, nloptr 2.1 MB.

Depends (1)

R >= 3.5.0

Imports (14)

config data.table futile.logger gmodels matrixcalc matrixStats nloptrparallelpbapply pracma rsvdstatsquadprogMatrix

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

lambda.r through futile.loggerdeadline passed Oct 12

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Elior Rahmani

Author, Maintainer since 1.0.0 (2019)

Brandon Jew

Contributor · added in 1.2.1

Releases (3)

Pick two releases to compare their code metrics.

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
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
1.2.1Latest
record
2021-02-14 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
record
2019-11-16 · diff ↗
1.0.0
record
2019-05-22
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-22
Total releases: 3 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 1.0 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("TCA")

The package provides a citation file, so citation() returns the authors' own entry.

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 TCA version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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