scellpam

1.4.7

Applying Partitioning Around Medoids to Single Cell Data with High Number of Cells

0packages depend

3.1Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Juan DomingoFirst published 2022-11-287 releasesCRAN page ↗

PAM (Partitioning Around Medoids) algorithm application to samples of single cell sequencing techniques with a high number of cells (as many as the computer memory allows). The package uses a binary format to store matrices (either full, sparse or symmetric) in files written in the disk that can contain any data type (not just double) which allows its manipulation when memory is sufficient to load them as int or float, but not as double. The PAM implementation is done in parallel, using several/all the cores of the machine, if it has them. This package shares a great part of its code with packages 'jmatrix' and 'parallelpam' but their functionality is included here so there is no need to install them.

Install

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

install.packages("scellpam", 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-scellpam

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-scellpam

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-scellpam

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 6.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-25
11 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

3.1K

CRAN downloads in the past year

Rank #7,480 · ~9/day · ~260/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

1.3K90 days

3.1K1 year

Compare downloads with other packages →

Also on394 r2u3 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

Rcpp memusecluster

LinkingTo (1)

Rcpp

Suggests (4)

rmarkdown knitr scater splatter

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Juan Domingo

Author, Maintainer

Authors (1)

Juan Domingo

Author, Maintainer

Contributors (1)

Guillermo Ayala

Contributor

Funders (1)

Spanish Ministry of Science and Innovation, MCIN/AEI <doi:10.13039/501100011033>

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.4.7Latest
2026-04-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.6.2
2024-07-18 · diff ↗
1.4.6.1
2024-07-03 · diff ↗
unarchivedReturned to CRAN
2024-07-03
archivedRemoved from CRAN
2024-07-02
issues were not corrected in time Intermittent issues on M1mac even on re-submission
R
R 4.4.0 released · 2024-04-24
1.4.5
2023-10-13 · diff ↗
1.4.4
2023-06-24 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.1
2023-01-09 · diff ↗
1.4
2022-11-28
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-11-28
Total releases: 7 / 4 yrs
License: GPL (>= 2) OSI
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →