PAC

1.1.6

Partition-Assisted Clustering and Multiple Alignments of Networks

0packages depend

3.5Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Ye Henry LiFirst published 2016-03-2516 releasesCRAN page ↗

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) doi:10.1371/journal.pcbi.1005875 for detail method description.

Install

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

install.packages("PAC", 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-pac

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-PAC

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-PAC

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: 2.9 min · r-oldrel-windows-x86_64

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 63%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #12,190 · ~10/day · ~295/mo

Releases R versions

Daily download trend is not available in this view yet.

26030 days

83190 days

3.5K1 year

Compare downloads with other packages →

Also on384 r2u1 autocran

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (8)

Rcpp igraph parmigene infotheo dplyr Rtsne ggplot2 ggrepel

LinkingTo (1)

Rcpp

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Ye Henry Li

Author, Maintainer · added in 1.0.6

Authors (2)

Ye Henry Li

Author, Maintainer · added in 1.0.6

Dangna Li

Author

Listed in earlier versions (2)

Henry Li

no longer listed · 1.0.0 to 1.0.5

no longer listed · 1.1.6

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.6Latest
2025-12-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.4
2021-02-18 · diff ↗
1.1.3
2020-12-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.2
2020-03-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
2019-01-03 · diff ↗
1.1.0
2018-10-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.10
2018-03-06 · diff ↗

Show 14 earlier events

unarchivedReturned to CRAN
2018-03-06
archivedRemoved from CRAN
2018-03-02
usage of archived package 'NMF' was unconditional
1.0.9
2017-08-16 · diff ↗
1.0.8
2017-04-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.7
2017-03-10 · diff ↗
1.0.6
2017-01-23 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.5
2016-04-10 · diff ↗
1.0.3
2016-03-29 · diff ↗
1.0.2
2016-03-29 · diff ↗
1.0.1
2016-03-27 · diff ↗
1.0.0
2016-03-25
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-03-25
Total releases: 16 / 10 yrs
License: GPL-3 OSI
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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