DEploid

0.5.7

Deconvolute Mixed Genomes with Unknown Proportions

0packages depend

2.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Joe ZhuFirst published 2016-11-2512 releasesCRAN page ↗GitHub ↗

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("DEploid", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("DEploid-dev/DEploid-r")

Development version from DEploid-dev/DEploid-r. Installs pak first if it is not already available.

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-deploid

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-DEploid

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 5.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 239 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 95%
Return-value docs: 50%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #16,151 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

23230 days

67190 days

2.7K1 year

Compare downloads with other packages →

Also on405 r2u

Repository

GitHub ↗ deploid-dev/deploid-r

1Stars

3Forks

12Open issues

0Open PRs

10Releases

267Commits

2Contributors

mcmcdeconvoluting-mixed-genomescranunknown-proportionshmmmalariaparasitesphasing

License GPL-3.0 · 267 commits · Last activity 2025-01-21

Stars over time

2020-05-25 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/deploid-dev/deploid-r on 2026-07-30.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

Git structural (2)

.gitattributesSubmodules

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.1.0DEploid.utils

Imports (6)

Rcpp scales plotly magrittr rmarkdown htmlwidgets

LinkingTo (1)

Rcpp

Suggests (2)

knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Joe Zhu

Author, Maintainer

Authors (3)

Joe Zhu

Author, Maintainer

Jacob Almagro-Garcia

Author · added in 0.4.2

Gil McVean

Author · added in 0.4.2

Contributors (1)

Yinghan Liu

Contributor · added in 0.4.2

University of Oxford

Deepak Bandyopadhyay

Compiler, Copyright holder · added in 0.4.2

Lutz Kettner

Compiler, Copyright holder · added in 0.4.2

CodeCogs Zyba Ltd

Compiler, Copyright holder · added in 0.4.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.5.7Latest
2025-01-20 · current release · diff ↗
0.5.6
2024-12-23 · diff ↗
0.5.4
2024-10-14 · diff ↗
unarchivedReturned to CRAN
2024-10-14
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
archivedRemoved from CRAN
2021-08-01
check problems were not corrected despite multiple reminders
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.5.3
2020-04-22 · diff ↗
unarchivedReturned to CRAN
2020-04-22
archivedRemoved from CRAN
2020-03-03
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26

Show 13 earlier events

0.5.2
2018-10-23 · diff ↗
0.5.1
2018-10-21 · diff ↗
unarchivedReturned to CRAN
2018-10-21
archivedRemoved from CRAN
2018-10-10
installation problems were not corrected despite reminders (and suggestions) Two separate compiler warnings, failure under clang trunk for include path conflicts
0.5.0
2018-05-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.4.4
2017-09-01 · diff ↗
0.4.3
2017-08-09 · diff ↗
0.4.2
2017-08-09 · diff ↗
0.4.1
2017-07-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.3.2
2016-11-25
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-11-25
Total releases: 12 / 10 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Download size: 928 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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