sccore

1.0.7

Core Utilities for Single-Cell RNA-Seq

5packages depend

43.1Kdownloads / year

3.1%test coverage

10/13checks pass

Overview

About

Maintained by Evan BiederstedtFirst published 2020-09-3012 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

3NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

3.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 95 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 100%
Return-value docs: 88%
References docs: 0%

Downloads

43.1K

CRAN downloads in the past year

Rank #1,966 · ~118/day · ~3.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.9K30 days

11.8K90 days

43.1K1 year

Compare downloads with other packages →

Also on741 r2u2 autocran7K conda_forge54 c2d4u

Repository

GitHub ↗ kharchenkolab/sccore

13Stars

3Forks

0Open issues

0Open PRs

11Releases

284Commits

7Contributors

284 commits · Last activity 2026-06-16 · 0% stars, 30d

Stars over time

2024-03-26 · 122026-07-07 · 13

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/kharchenkolab/sccore on 2026-07-31.

Continuous integration (2)

Travis CICircleCI

Reproducibility and dev environment (1)

data-raw/

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

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

5direct

2indirect

CRMetrics conos leidenAlg pagoda2 scITD

Code & Tests

People & History

People (4)

Maintainer (1)

Evan Biederstedt

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author · added in 1.0.4

Listed in earlier versions (1)

Ramus Rydbirk

no longer listed · 0.1.0 to 1.0.3

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
2026-04-06 · current release · diff ↗
1.0.6
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
2024-02-23 · diff ↗
1.0.4
2023-07-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.3
2023-03-13 · diff ↗
1.0.2
2022-08-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
2021-12-12 · diff ↗
1.0.0
2021-10-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.3
2021-05-05 · diff ↗
0.1.2
2021-02-23 · diff ↗

Show 3 earlier events

0.1.1
2020-12-14 · diff ↗
0.1.0
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: 370 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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