R Observatory: Metrics for scISR version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scISR

0.1.1Package record

Single-Cell Imputation using Subspace Regression

0packages depend

2.2Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Duc TranCRAN page ↗GitHub ↗Issues ↗Declared funder: Tin Nguyen

Provides an imputation pipeline for single-cell RNA sequencing data. The 'scISR' method uses a hypothesis-testing technique to identify zero-valued entries that are most likely affected by dropout events and estimates the dropout values using a subspace regression model (Tran et.al. (2022) DOI:10.1038/s41598-022-06500-4).

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("scISR", 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("duct317/scISR")

Development version from duct317/scISR. 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-scisr

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

Health

CRAN checks

4NOTE9OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Duc Tran <duct@nevada.unr.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘markdown’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTENow
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 177 wordsVignettesYes · 1 · staticNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

scISR package manual

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #20,239 · ~6/day · ~183/mo

Releases R versions

Daily download trend is not available in this view yet.

21230 days

65990 days

2.2K1 year

Compare downloads with other packages →

Also on74 r2u

How downloads are counted

Repository

duct317/scisr ↗Account: duct317

3Stars

2Forks

2Open issues

0Open PRs

0Releases

14Commits

2Commit identities

14 commits · Last activity 2022-06-30 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-07-26 · 32026-07-07 · 3

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/duct317/scisr on 2026-10-21.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing scISR adds 16 packages (10 with compiled code, 8.6 MB of source tarballs). Heaviest: mclust 2.7 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.4

Imports (9)

clusterentropystatsutilsparallelirlba PINSPlus matrixStats markdown

LinkingTo (0)

none

Suggests (3)

testthat knitr mclust

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 (4)

Duc Tran

Author, Maintainer since 0.1.1 (2022)

Hung Nguyen

Author

Bang Tran

Author

Tin Nguyen

Funder

Releases (1)

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
R
R 4.3.0 released · 2023-04-21
0.1.1Latest
record
2022-06-30 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-30
Total releases: 1 / 4 yrs
License: LGPL
Minimum R: ≥ 3.4
Bundled data: 569 KB / 1 file
Download size: 588 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("scISR")

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

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 scISR version 0.1.1 [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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