R Observatory: Metrics for sccore version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sccore

1.0.7Package record

Core Utilities for Single-Cell RNA-Seq

4packages depend

43.2Kdownloads / year

3.1%test coverage

11/13flavors OK

Overview

About

Maintained by Evan BiederstedtCRAN page ↗GitHub ↗Issues ↗

Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP doi:10.21105/joss.00861, collapsing vertices of each cluster in the graph, and propagating graph labels.

Install

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

install.packages("sccore", 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("kharchenkolab/sccore")

Development version from kharchenkolab/sccore. 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-sccore

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-sccore

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-sccore

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

2NOTE11OK

Check messages

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

Namespaces in Imports field not imported from:
  ‘tibble’ ‘utils’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE10 OK, 4 NOTE2026-04-22
ERROR9 OK, 4 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 4 NOTE2026-04-10
ERROR9 OK, 4 NOTE, 1 ERROR2026-04-09
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 95 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Description cites a JOSS paper

Help pages: 45 (2 internal)
Examples that run: 67%14 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run
Exported functions with examples: 69%
Documented parameters: 100%
Return-value docs: 88%
Help pages citing references: 0%

How these are measured

Downloads

43.2K

CRAN downloads in the past year

Rank #1,649 · ~118/day · ~3.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.1K30 days

13.4K90 days

43.2K1 year

Compare downloads with other packages →

Also on1.5K r2u6 autocran7.1K conda_forge69 c2d4u

How downloads are counted

Repository

kharchenkolab/sccore ↗Organization: kharchenkolab

13Stars

3Forks

0Open issues

0Open PRs

11Releases

284Commits

7Commit identities

284 commits · Last activity 2026-04-06 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 29
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2024-03-26 · 122026-07-07 · 13

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/kharchenkolab/sccore on 2026-10-18.

Continuous integration (2)

Travis CI (config file)CircleCI

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing sccore adds 41 packages (26 with compiled code, 42 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

R >= 3.5.0

Imports (21)

dplyr ggplot2 ggrepelgraphicsgrDevicesigraph irlba magrittrMatrixmethodsparallelpbmcapply pROC Rcpp rlang scalesstatstibbleutilsuwot withr

LinkingTo (4)

Rcpp RcppArmadillo RcppProgress RcppEigen

Suggests (6)

ggrastr jsonlite philentropy rmumps Seurat testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

2indirect

Imports 4

Depends, Imports or LinkingTo, most downloaded first

leidenAlg pagoda2 conos CRMetrics

How these are counted

Code & Tests

Datasets

People & History

People (4)

Evan Biederstedt

Author, Maintainer since 0.1.0 (2020)

Peter Kharchenko

Author

Viktor Petukhov

Author

Rasmus Rydbirk

Author · added in 1.0.4

Listed in earlier versions (1)

Ramus Rydbirk

no longer listed · 0.1.0 to 1.0.3

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
record
2026-04-06 · current release · diff ↗
1.0.6
record
2025-04-13 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.5
record
2024-02-23 · diff ↗
1.0.4
record
2023-07-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.3
record
2023-03-13 · diff ↗ ·
added 2 exports
checkPackageInstalled, saveDeAsJson
1.0.2
record
2022-08-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
record
2021-12-12 · diff ↗ ·
added 1 export
heatFilter
1.0.0
record
2021-10-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.3
record
2021-05-05 · diff ↗ ·
added 1 export
collapseCellsByType
0.1.2
record
2021-02-23 · diff ↗ ·
added 2 exports
smoothSignalOnGraph, val2col

Show 3 earlier eventsHide 3 earlier events

0.1.1
record
2020-12-14 · diff ↗
0.1.0
record
2020-09-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-30
Total releases: 12 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 313 KB / 4 files
Download size: 372 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sccore")

Format

Biederstedt, E., Kharchenko, P., Petukhov, V., & Rydbirk, R. (2026). sccore: Core Utilities for Single-Cell RNA-Seq (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.sccore

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 sccore version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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