mappoly

Genetic maps in autopolyploids

https://github.com/mmollina/mappoly

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 40 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
2 of 8 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary

Keywords

polyploid polyploid-genetic-mapping polyploidy

Keywords from Contributors

qtl-mapping

Last synced: 6 months ago · JSON representation

Repository

Genetic maps in autopolyploids

Basic Info

Host: GitHub
Owner: mmollina
Language: R
Default Branch: main
Homepage:
Size: 382 MB

Statistics

Stars: 29
Watchers: 6
Forks: 9
Open Issues: 11
Releases: 8

Topics

polyploid polyploid-genetic-mapping polyploidy

Created almost 8 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog

MAPpoly

MAPpoly (v. 0.4.1) is an R package to construct genetic maps in diploids and autopolyploids with even ploidy levels. In its current version, MAPpoly can handle ploidy levels up to 8 when using hidden Markov models (HMM) and up to 12 when using the two-point simplification. When dealing with large numbers of markers (> 10,000), we strongly recommend using high-performance computing (HPC).

In its current version, MAPpoly can handle the following types of datasets:

CSV files
MAPpoly files
- Dosage based
- Probability based
fitPoly files
VCF files

MAPpoly also is capable of importing objects generated by the following R packages

updog
polyRAD
polymapR
- Datasets
- Maps

The mapping strategy uses pairwise recombination fraction estimation as the first source of information to position allelic variants in specific homologs sequentially. The algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM) for situations where pairwise analysis has limited power. The derivation of the HMM used in MAPpoly can be found in Mollinari and Garcia, 2019. The computation of the offspring's genotypes probabilities and haplotype reconstruction, as well as the preferential pairing profiles, is presented in Mollinari et al., 2020.

Installation

From CRAN (stable version)

To install MAPpoly from the The Comprehensive R Archive Network (CRAN) use

R install.packages("mappoly")

From GitHub (development version)

You can install the development version from Git Hub. Within R, you need to install devtools:

R install.packages("devtools")

If you are using Windows, please install the the latest recommended version of Rtools.

To install MAPpoly from Git Hub use

R devtools::install_github("mmollina/mappoly", dependencies=TRUE)

For further QTL analysis, we recommend our QTLpoly package. QTLpoly performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. 2020.

We recently released VIEWpoly. VIEWpoly provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid (and diploid) species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. VIEWpoly supports inputs other than MAPpoly's, including polymapR, diaQTL, QTLpoly, and polyqtlR.

MAPpoly's workflow

Vignettes

To access the MAPpoly vignette from R, use R vignette("mappoly_startguide")
Building a genetic map in a tetraploid potato full-sib population using MAPpoly
Building a genetic map in an hexaploid full-sib population using MAPpoly
Real datasets
Simulated datasets
- Hexaploid simulation with dosage call in MAPpoly format
- Hexaploid simulation with dosage probabilities in MAPpoly format

Related software

Polyverse - the polyploid R universe (a Lindsay Clark's initiative) ```R # Enable this universe options(repos = c( polyploids = 'https://polyploids.r-universe.dev', CRAN = 'https://cloud.r-project.org'))

Install some packages

install.packages('mappoly') ```

Miscellaneous

Articles referencing MAPpoly

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations (Lau et al., 2022)
VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. (Taniguti et al., 2022)
Genetic Dissection of Early Blight Resistance in Tetraploid Potato. (Xue et al., 2022)
Haplotype reconstruction in connected tetraploid F1 populations (Zheng et al., 2021)
QTL mapping in outbred tetraploid (and diploid) diallel populations (Amadeu et al., 2021)
Using probabilistic genotypes in linkage analysis of polyploids. (Liao et al., 2021)
Discovery of a major QTL for root-knot nematode Meloidogyne incognita resistance in cultivated sweetpotato Ipomoea batatas. (Oloka, et al., 2021)
Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population. (Pereira et al., 2021)
The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv.'Atlantic'-derived F1 population. (Pereira et al., 2021)
High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry (Cappai et al., 2020)
When a phenotype is not the genotype: Implications of phenotype misclassification and pedigree errors in genomics-assisted breeding of sweetpotato Ipomoea batatas (L.) Lam.(Gemenet et al., 2020)
Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated beta-carotene and starch content in hexaploid sweetpotato Ipomoea batatas (L.) Lam.
Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population. (Pereira et al., 2020)

Acknowledgment

This package has been developed as part of the Genomic Tools for Sweetpotato Improvement project (GT4SP) and SweetGAINS, both funded by Bill & Melinda Gates Foundation. Its continuous improvement is made possible by the project AFRI-Grant: A Genetics-Based Data Analysis System for Breeders in Polyploid Breeding Programs and SCRI-Grant: Tools for polyploids, funded by USDA NIFA.

_{NC State University promotes equal opportunity and prohibits discrimination and harassment based upon one’s age, color, disability, gender identity, genetic information, national origin, race, religion, sex (including pregnancy), sexual orientation and veteran status.}

Owner

Name: Marcelo Mollinari
Login: mmollina
Kind: user
Location: USA
Company: North Carolina State University

Repositories: 5
Profile: https://github.com/mmollina

Research Assistant Professor - Bioinformatics Research Center - Department of Horticultural Science

GitHub Events

Total

Create event: 1
Release event: 1
Issues event: 2
Watch event: 6
Push event: 27

Last Year

Create event: 1
Release event: 1
Issues event: 2
Watch event: 6
Push event: 27

Committers

Last synced: over 2 years ago

All Time

Total Commits: 774
Total Committers: 8
Avg Commits per committer: 96.75
Development Distribution Score (DDS): 0.311

Past Year

Commits: 77
Committers: 4
Avg Commits per committer: 19.25
Development Distribution Score (DDS): 0.182

Top Committers

Name	Email	Commits
Marcelo Mollinari	m**a@g**m	533
Marcelo Mollinari	m**a@G**M	107
“gabrielgesteira”	“**a@g**”	67
gabrielgesteira	g**a@g**m	48
Jeekin Lau	j**u@g**m	9
Cristianetaniguti	c**i@g**m	6
Marcelo Mollinari	m**n@n**u	3
Cristianetaniguti	c**i@t**u	1

Committer Domains (Top 20 + Academic)

tamu.edu: 1 ncsu.edu: 1 gmail.com”: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 26
Total pull requests: 50
Average time to close issues: 2 months
Average time to close pull requests: 4 days
Total issue authors: 18
Total pull request authors: 5
Average comments per issue: 3.04
Average comments per pull request: 0.34
Merged pull requests: 45
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

jeekinlau (3)
baozg (3)
rramadeu (2)
wittney (2)
KillianLrnt (2)
mmollina (2)
alinedclm (1)
PhiliptheoD (1)
bechee (1)
wrengs (1)
VianeiRother (1)
kaurharpreet-umn (1)
behling3 (1)
PaulaEB (1)
jxandyq (1)

Pull Request Authors

gabrielgesteira (32)
Cristianetaniguti (8)
mmollina (7)
jeekinlau (2)
jeroen (2)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 396 last-month

Total dependent packages: 3
Total dependent repositories: 1
Total versions: 9
Total maintainers: 1

cran.r-project.org: mappoly

Genetic Linkage Maps in Autopolyploids

Homepage: https://github.com/mmollina/MAPpoly
Documentation: http://cran.r-project.org/web/packages/mappoly/mappoly.pdf
License: GPL-3
Latest release: 0.4.1
published almost 2 years ago

Versions: 9
Dependent Packages: 3
Dependent Repositories: 1
Downloads: 396 Last month

Rankings

Forks count: 7.3%

Dependent packages count: 10.9%

Stargazers count: 11.5%

Average: 19.0%

Dependent repos count: 23.8%

Downloads: 41.3%

Maintainers (1)

mmollin@ncsu.edu

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 4.0.0 depends
RCurl * imports
Rcpp >= 0.12.6 imports
RcppParallel * imports
cli * imports
crayon * imports
dendextend * imports
dplyr * imports
fields * imports
ggplot2 * imports
ggpubr * imports
ggsci * imports
magrittr * imports
plotly * imports
princurve * imports
reshape2 * imports
rstudioapi * imports
scatterplot3d * imports
vcfR * imports
zoo * imports
AGHmatrix * suggests
fitPoly * suggests
gatepoints * suggests
knitr * suggests
polymapR * suggests
rmarkdown * suggests
smacof * suggests
testthat * suggests
updog * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
actions/setup-node v1 composite
actions/upload-artifact main composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

mappoly

Science Score: 46.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

MAPpoly

Installation

From CRAN (stable version)

From GitHub (development version)

MAPpoly's workflow

Vignettes

Related software

Install some packages

Miscellaneous

Articles referencing MAPpoly

Acknowledgment

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: mappoly

Rankings

Maintainers (1)

Dependencies