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

0.1.0Package record

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

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by XinWangCRAN 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)

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.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 126 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 22
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

pulseTD Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on41 r2u

How downloads are counted

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

XinWang

Contributor

Maintainer since 0.1.0 (2019)

Releases (1)

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
record
2019-05-17
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-17
Total releases: 1 / 7 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.4.0
Bundled data: 1.3 MB / 5 files

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 October 25, 2026, from https://CRAN.R-project.org/package=pulseTD

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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