R Observatory: Metrics for SlideCNA version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SlideCNA

0.1.0

Calls Copy Number Alterations from Slide-Seq Data

0packages depend

2.3Kdownloads / year

3.7%test coverage

13/13checks pass

Overview

About

Maintained by Diane ZhangFirst published 2025-01-231 releasesCRAN page ↗

This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, doi:10.1101/2022.11.25.517982). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at https://github.com/wjawaid/enrichR or with install_github("wjawaid/enrichR").

Install

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

install.packages("SlideCNA", 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-slidecna

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-SlideCNA

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-SlideCNA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.11

3.7%

Coverage · measured lines

96%

Documentation · exports

17

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 456 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 98%
Return-value docs: 96%
References docs: 0%

Downloads

2.3K

CRAN downloads in the past year

Rank #20,638 · ~6/day · ~192/mo

Releases R versions

Daily download trend is not available in this view yet.

15530 days

53990 days

2.3K1 year

Compare downloads with other packages →

Also on103 r2u2 autocran402 conda_forge

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (17)

data.table reshape2 dplyr ggplot2 scales pheatmapclusterfactoextra dendextend Seurat tidyselect stringr magrittr tibble futile.logger mltoolsutils

LinkingTo (0)

none

Suggests (2)

testthat enrichR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Diane Zhang

Author, Maintainer

Authors (3)

Diane Zhang

Author, Maintainer

Johanna Klughammer

Author

Jan Watter

Author

Copyright holders (1)

Broad Institute of MIT and Harvard

Copyright holder, Funder

Funders (1)

Broad Institute of MIT and Harvard

Copyright holder, Funder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-01-23
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Download size: 39 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SlideCNA")

Format

Zhang, D., Broad Institute of MIT and Harvard, Klughammer, J., & Watter, J. (2025). SlideCNA: Calls Copy Number Alterations from Slide-Seq Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SlideCNA

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 SlideCNA version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →