scquantum

1.0.0

Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing

0packages depend

2.2Kdownloads / year

88.7%test coverage

10/13checks pass

Overview

About

Maintained by Alexander DavisFirst published 2022-03-231 releasesCRAN page ↗

Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) doi:10.1002/0471667196.ess2129.pub2, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) doi:10.1080/10618600.2012.681238, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.

Install

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

install.packages("scquantum", 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-scquantum

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-scquantum

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-scquantum

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: 52 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

88.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 75 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 50%
Return-value docs: 50%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #19,283 · ~6/day · ~185/mo

Releases R versions

Daily download trend is not available in this view yet.

16930 days

57590 days

2.2K1 year

Compare downloads with other packages →

Also on384 r2u2 autocran

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Alexander Davis

Author, Maintainer

Authors (1)

Alexander Davis

Author, Maintainer

Taylor Arnold

Veeranjaneyulu Sadhanala

Ryan Tibshirani

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-03-23
Total releases: 1 / 4 yrs
License: GPL (>= 2) OSI
Download size: 11 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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