SlideCNA

0.1.0

Calls Copy Number Alterations from Slide-Seq Data

0packages depend

2.4Kdownloads / 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: 2.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.11

3.7%

Coverage · measured lines

96%

Documentation · exports

Dependencies · direct

Check history

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
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

2.4K

CRAN downloads in the past year

Rank #21,465 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

15530 days

56390 days

2.4K1 year

Compare downloads with other packages →

Also on99 r2u4 autocran411 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

Code Composition

R 2,413 (73%)Rd 883 (27%)

Code characteristics

Cyclomatic complexity: 2.0 median / 15 max
Test cases: 8 / 0.11 per code line

Test coverage

Line coverage

Expression

6.2%

Tests / Examples

3.7% / 0% ex

Functions

26 26 exported

Complexity

3.5 avg / 15 max

Call network

26 nodes / 27 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

26 functions

Function	Cyclo	Coverage
SpatialPlot exp	11	0%
bin exp	2	0%
bin_metadata exp	1	0%
center_rm exp	1	0%
clone_so exp	2	0%
cnv_heatmap exp	1	0%

People & History

People (4)

Maintainer (1)

Diane Zhang

Author, Maintainer

Authors (3)

Diane Zhang

Author, Maintainer

Johanna Klughammer

Author

Jan Watter

Author

Broad Institute of MIT and Harvard

Funders (1)

Broad Institute of MIT and Harvard

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

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