R Observatory: Metrics for SurprisalAnalysis version 3.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SurprisalAnalysis

3.0.1Package record

Information Theoretic Analysis of Gene Expression Data

0packages depend

4.3Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Annice NajafiCRAN page ↗

Implements Surprisal analysis for gene expression data such as RNA-seq or microarray experiments. Surprisal analysis is an information-theoretic method that decomposes gene expression data into a baseline state and constraint-associated deviations, capturing coordinated gene expression patterns under different biological conditions. References: Kravchenko-Balasha N. et al. (2014) doi:10.1371/journal.pone.0108549. Zadran S. et al. (2014) doi:10.1073/pnas.1414714111. Su Y. et al. (2019) doi:10.1371/journal.pcbi.1007034. Bogaert K. A. et al. (2018) doi:10.1371/journal.pone.0195142.

Install

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

install.packages("SurprisalAnalysis", 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-surprisalanalysis

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-SurprisalAnalysis

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.3 min · r-oldrel-windows-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 OK2026-04-30

Show 1 earlier changeHide 1 earlier change

ERROR9 OK, 2 NOTE, 3 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0.1

READMEYes · 131 wordsVignettesYes · 3 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3
Examples that run: 100%3 run in a plain check (1 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #6,780 · ~12/day · ~361/mo

Releases R versions

Daily download trend is not available in this view yet.

68030 days

1.2K90 days

4.3K1 year

Compare downloads with other packages →

Also on97 r2u

How downloads are counted

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing SurprisalAnalysis adds 100 packages (50 with compiled code, 92 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (0)

none

Imports (8)

matlib shiny ggplot2 shinythemes shinyjs shinycssloaders patchwork DT

LinkingTo (0)

none

Suggests (11)

knitr rmarkdown pheatmap peakRAM data.table BiocManager clusterProfiler AnnotationDbi org.Hs.eg.db org.Mm.eg.db httpuv

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 (1)

Annice Najafi

Author, Maintainer since 0.2 (2025)

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.0.1Latest
record
2026-04-23 · current release · diff ↗
3.0.0
record
2026-01-08 · diff ↗
0.2
record
2025-09-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-10
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 2.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SurprisalAnalysis")

Format

Najafi, A. (2026). SurprisalAnalysis: Information Theoretic Analysis of Gene Expression Data (Version 3.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SurprisalAnalysis

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 SurprisalAnalysis version 3.0.1 [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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