R Observatory: Metrics for TTCA version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

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

TTCA

0.1.1Package record

Transcript Time Course Analysis

0packages depend

2.3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Marco AlbrechtCRAN page ↗

The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)DOI:10.1186/s12859-016-1440-8.

Install

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

install.packages("TTCA", 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-ttca

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-TTCA

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-TTCA

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

2NOTE11OK

Check messages

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

Maintainer: ‘Marco Albrecht <marco.albrecht@posteo.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Marco",
                    family = "Albrecht",
                    role = c("aut", "cre"),
                    email = "marco.albrecht@posteo.de")
as necessary.

CRAN check page ↗

Slowest check: 3.4 min · r-oldrel-macos-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 80%4 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #18,035 · ~6/day · ~192/mo

Releases R versions

Daily download trend is not available in this view yet.

35030 days

70590 days

2.3K1 year

Compare downloads with other packages →

Also on78 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing TTCA adds 21 packages (11 with compiled code, 7.3 MB of source tarballs). Heaviest: openssl 1.1 MB, tcltk2 1.1 MB, jsonlite 1.0 MB.

Depends (1)

R >= 2.10

Imports (6)

Matrixquantreg tcltk2 RISmed VennDiagramMASS

LinkingTo (0)

none

Suggests (0)

none

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 VennDiagram → futile.loggerdeadline passed Oct 12

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Marco Albrecht

Maintainer since 0.1.0 (2016)

Releases (2)

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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
0.1.1Latest
record
2017-01-29 · current release · diff ↗
0.1.0
record
2016-06-20
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-06-20
Total releases: 2 / 10 yrs
License: EUPL
Minimum R: ≥ 2.10
Bundled data: 1.1 MB / 5 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TTCA")

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 TTCA version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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