R Observatory: Metrics for RNAseqNet version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RNAseqNet

0.1.5Package record

Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nathalie VialaneixCRAN page ↗

Infer log-linear Poisson Graphical Model with an auxiliary data set. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset. Standard log-linear Poisson graphical model can also be used for the inference and the Stability Approach for Regularization Selection (StARS) is implemented to drive the selection of the regularization parameter. The method is fully described in doi:10.1093/bioinformatics/btx819.

Changes in 0.1.5

misc
fixed CRAN notes (removed itemize from documentation)
rewrote NEWS file (new format)
rewrote CITATION file (new format)

From NEWS.md in the release

Install

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

install.packages("RNAseqNet", 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-rnaseqnet

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-RNAseqNet

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-RNAseqNet

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

13OK

CRAN check page ↗

Slowest check: 2.7 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.5Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 100%8 run in a plain check
Exported functions with examples: 88%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (1)

Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #12,859 · ~9/day · ~282/mo

Releases R versions

Daily download trend is not available in this view yet.

30930 days

87290 days

3.4K1 year

Compare downloads with other packages →

Also on90 r2u4 autocran155 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing RNAseqNet adds 66 packages (36 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 3.1.0ggplot2

Imports (6)

igraph hot.deck PoiClaClu glmnetmethodsutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Nathalie Vialaneix

Author, Maintainer · added in 0.1.3

Alyssa Imbert

Author

Maintainer since 0.1.0 (2017)

Listed in earlier versions (1)

Nathalie Villa-Vialaneix

no longer listed · 0.1.0 to 0.1.2

Releases (6)

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
0.1.5Latest
record
2024-02-20 · current release · diff ↗
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
0.1.4
record
2020-06-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.3
record
2020-03-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.2
record
2018-01-19 · diff ↗
0.1.1
record
2017-05-16 · diff ↗ ·
added 1 export
RNAseqNetUsersGuide
R
R 3.4.0 released · 2017-04-21
0.1.0
record
2017-04-19

Show 1 earlier eventHide 1 earlier event

R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-04-19
Total releases: 6 / 9 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Bundled data: 255 KB / 2 files
Download size: 1.4 MB

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("RNAseqNet")

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

It points to 10.1093/bioinformatics/btx819.

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 RNAseqNet version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, 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 →