R Observatory: Metrics for splikit version 2.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

splikit

2.3.1Package record

Analysing RNA Splicing in Single-Cell RNA Sequencing Data

0packages depend

1.8Kdownloads / year

28.6%test coverage

13/13flavors OK

Overview

About

Maintained by Arsham Mikaeili NaminiCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides analysis of high-dimensional single-cell splicing data. Offers a framework to extract and work with ratio-based data structures derived from single-cell RNA sequencing experiments. Provides both a modern 'R6' object-oriented interface and direct matrix manipulation functions. Core functionalities are implemented in 'C++' via 'Rcpp' to ensure high performance and scalability on large datasets.

Changes in 2.3.1

CRAN Compliance

Fixed no visible binding for '..keep' NOTE in .gene_exons(): replaced exons[, ..keep] with exons[, keep, with = FALSE].
Fixed no visible binding for 'x' NOTE in .build_plot(): added x to globalVariables() in globals.R.
Wrapped get_pseudo_correlation() example in \donttest{} to avoid exceeding the CRAN 5-second example time limit.

From NEWS.md in the release

Install

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

install.packages("splikit", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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

Development version from csglab/splikit. 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-splikit

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-splikit

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-splikit

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: 5.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-14

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.1

READMEYes · 275 wordsVignettesYes · 3 · staticNEWSYes · 100% structured · mentions 2.3.1Citation fileNoWebsiteYes · pkgdown

Help pages: 22 (3 internal)includes a package overview page
Examples that run: 60%6 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 56%
Documented parameters: 90%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #15,577 · ~5/day · ~151/mo

Releases R versions

Daily download trend is not available in this view yet.

25730 days

78890 days

1.8K1 year

Compare downloads with other packages →

Also on108 r2u4 autocran

How downloads are counted

Repository

csglab/splikit ↗Organization: csglab

2Stars

0Forks

1Open issues

0Open PRs

6Releases

193Commits

1Commit identities

rna-splicingsingle-cell-gecran

193 commits · Last activity 2026-07-30 · 0% stars, 30d · Default branch at 2.3.3, ahead of CRAN 2.3.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-01-14 · 12026-07-07 · 2

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/csglab/splikit on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (1)

Issue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-30 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2025-11-16
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: .claude, CLAUDE.md
Pull request it wrote: opened by a project member

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing splikit adds 4 packages (3 with compiled code, 8.6 MB of source tarballs). Heaviest: data.table 5.7 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (1)

R >= 4.1.0

Imports (6)

Matrixdata.tablemethodsstatsRcpp R6

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

testthat knitr rmarkdown ggplot2

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)

Arsham Mikaeili Namini

Author, Maintainer since 2.3.1 (2026)

Releases (1)

2.3.1Latest
record
2026-05-13 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-13
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 5.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("splikit")

Format

Mikaeili Namini, A. (2026). splikit: Analysing RNA Splicing in Single-Cell RNA Sequencing Data (Version 2.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.splikit

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 splikit version 2.3.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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