R Observatory: Metrics for NBBttest version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-04-20. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.0.1, its last release before removal.

NBBttest

1.0.1

Negative Binomial Beta t-Test

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Yuan-De Tan2 releasesCRAN page ↗

We constructed 'NBBttest' for identifying genes or RNA isoforms differentially expressed between two conditions on RNA-seq count data. Package 'NBBttest' can perform data quality check, data normalization, differential analysis, annotation and graphic analysis. In differential analysis, 'NBBttest' can identify differentially expressed genes and differential RNA isoforms in alternative splicing sites and alternative polyadenylation sites, differential sgRNA, and differential CRISPR (clustered regularly interspaced short palindromic repeats) screening genes. In graphic analysis, 'NBBttest' provides two types of heatmaps to visualize differential expression at gene or isoform level using z-score and n-score and creates pathway heatmap. 'NBBttest' can plot differentially expressed exons within a specified gene. In addition, 'NBBttest' provides a tool for annotation of genes and exons. The methods used in 'NBBttest' were new statistical methods developed from Tan and others (2015) doi:10.1371/journal.pone.0123658. The statistical methods are robust and very powerful in identifying genes or RNA isoforms differentially expressed between two conditions in small samples.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/NBBttest/NBBttest_1.0.1.tar.gz"
pkgFile <- "NBBttest_1.0.1.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 (1.0.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-nbbttest

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

# 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-NBBttest

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

6

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 53%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on99 r2u14 autocran34 c2d4u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (7)

R >= 3.5.0gplots gtoolsstatsutilsgraphicsgrDevices

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

BiocGenerics DEXSeq

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Other (1)

Yuan-De Tan

Contributor

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected despite reminders
R
R 4.3.0 released · 2023-04-21
1.0.1
2022-05-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0
2020-06-25
R
R 4.0.0 released · 2020-04-24

Package metadata

Total releases: 2
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.3 MB / 12 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("NBBttest")

Format

Tan, Y. (n.d.). NBBttest: Negative Binomial Beta t-Test (Version 1.0.1) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=NBBttest

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 NBBttest version 1.0.1 [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.

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