R Observatory: Metrics for pulseTD version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-05-04. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 0.1.0, its last release before removal.

pulseTD

0.1.0

Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by XinWang1 releasesCRAN page ↗GitHub ↗

A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq (the Metabolic Label 4-thiouridine) data and RNA-seq (RNA sequencing) data. It can not only recognize the transcriptional dynamic rates at the measurement time points, but also obtain continuous changes in transcriptional dynamics. More importantly, it is able to predict the trend of mRNA (Mature RNA) transcription and expression changes in the future.

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/pulseTD/pulseTD_0.1.0.tar.gz"
pkgFile <- "pulseTD_0.1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("bioWzz/pulseTD_0.1.0")

Development version from bioWzz/pulseTD_0.1.0. 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-pulsetd

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

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Documentation

READMEYes · 126 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

pulseTD Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on99 r2u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (11)

AnnotationDbi SummarizedExperiment Rsamtools Biobase S4VectorsmethodsparallelGenomicFeatures ggplot2gridGenomicAlignments

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown TxDb.Hsapiens.UCSC.hg19.knownGene

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Other (1)

XinWang

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-05-04
issues were not corrected in time
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
0.1.0
2019-05-17
R
R 3.6.0 released · 2019-04-26

Package metadata

Total releases: 1
License: GPL-2 OSI
Minimum R: ≥ 3.4.0
Bundled data: 1.3 MB / 5 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pulseTD")

Format

XinWang, . (n.d.). pulseTD: Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data (Version 0.1.0) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=pulseTD

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 pulseTD version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →