scShardSplitRef

0.1.0

Build Custom Reference Genome for Single-Cell Multiome ATAC and Gene Expression Data of Large-Genome Species

0packages depend

120downloads / year

64.9%test coverage

12/13checks pass

Overview

About

Maintained by Irina KuznetsovaFirst published 2026-07-231 releasesCRAN page ↗

Provides utilities that enable researchers to build custom references for the Multiome ATAC Gene Expression sequencing data for large-genome species without manual intervention.

Install

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

install.packages("scShardSplitRef", 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-scshardsplitref

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-scShardSplitRef

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

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 3.6 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.60

64.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-24
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 904 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

120

CRAN downloads in the past year

Rank #24,495 · ~0/day · ~10/mo

Releases R versions

Daily download trend is not available in this view yet.

12030 days

12090 days

1201 year

Compare downloads with other packages →

Also on5 r2u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (5)

cli rlang stringiutilswithr

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown roxyglobals testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Irina Kuznetsova

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Funder, Copyright holder

Grains Research and Development Corporation

Funder, Copyright holder

Funders (2)

Curtin University

Funder, Copyright holder

Grains Research and Development Corporation

Funder, Copyright holder

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-07-23 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-23
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.3.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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