pcadapt

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

https://github.com/bcm-uga/pcadapt

Science Score: 33.0%

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
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.zenodo.json file
✓
DOI references
Found 9 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
1 of 10 committers (10.0%) 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 (7.8%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

Basic Info

Host: GitHub
Owner: bcm-uga
Language: R
Default Branch: master
Homepage: https://bcm-uga.github.io/pcadapt
Size: 18.9 MB

Statistics

Stars: 42
Watchers: 2
Forks: 10
Open Issues: 0
Releases: 0

Created almost 10 years ago · Last pushed 12 months ago

Metadata Files

Readme

README.md

pcadapt

R package {pcadapt} was developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA).

A tutorial for {pcadapt} is available on pcadapt's website.

News: Our paper describing version 4 of pcadapt (which has been available for quite some time now) is out. Please cite the newest paper (see Refs below).

Installation

```r

From CRAN

install.packages("pcadapt")

From GitHub

remotes::install_github("bcm-uga/pcadapt") ```

References

Privé, F., Luu, K., Vilhjálmsson, B. J., & Blum, M. G.B. (2020). Performing highly efficient genome scans for local adaptation with R package pcadapt version 4. Molecular Biology and Evolution 37.7 (2020): 2153–2154.
Luu, K., Bazin, E., & Blum, M. G.B. (2017). pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources, 17(1), 67–77.
Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E., & Blum, M. G.B. (2015). Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular biology and evolution, 33(4), 1082–1093.

Owner

Name: Mathematical and Computational Biology Research Group
Login: bcm-uga
Kind: organization
Location: Grenoble

Website: http://www-timc.imag.fr/rubrique44.html
Repositories: 17
Profile: https://github.com/bcm-uga

Team of Mathematical and Computational Biology at Univ Grenoble Alpes (France).

GitHub Events

Total

Issues event: 11
Watch event: 3
Issue comment event: 18
Push event: 1

Last Year

Issues event: 11
Watch event: 3
Issue comment event: 18
Push event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 332
Total Committers: 10
Avg Commits per committer: 33.2
Development Distribution Score (DDS): 0.331

Past Year

Commits: 5
Committers: 1
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
keurcien	k**u@g**m	222
Florian Privé	f**1@g**m	78
mblumuga	m**m@i**r	14
Michael Blum	m**m@u**r	8
cayek	k**e@g**m	3
Florian Privé	f**e@i**g	2
Florian Franck Privé	a**3@u**k	2
kevin Caye	k**a@c**r	1
privef	p**f@t**r	1
jbruxaux	5****x	1

Committer Domains (Top 20 + Academic)

timc-bcm-30.imag.fr: 1 club-internet.fr: 1 uni.au.dk: 1 inp-grenoble.org: 1 univ-grenoble-alpes.fr: 1 imag.fr: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 93
Total pull requests: 6
Average time to close issues: 5 months
Average time to close pull requests: 11 minutes
Total issue authors: 77
Total pull request authors: 4
Average comments per issue: 6.09
Average comments per pull request: 0.17
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 7
Pull requests: 0
Average time to close issues: 5 months
Average time to close pull requests: N/A
Issue authors: 7
Pull request authors: 0
Average comments per issue: 3.57
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Ella-Bowles (5)
devonorourke (4)
keurcien (3)
jpfontenelle (3)
Mary-00 (3)
zillurbmb51 (2)
apfuentes (2)
fvaux (2)
ewmorr (1)
shaghayeghsoudi (1)
naborlozada (1)
cyadrogarcia (1)
peuclide (1)
j-a-thia (1)
kbcn (1)

Pull Request Authors

keurcien (2)
mblumuga (2)
jbruxaux (1)
privefl (1)

Top Labels

Issue Labels

wontfix (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 968 last-month
Total docker downloads: 1,549

Total dependent packages: 1
Total dependent repositories: 2
Total versions: 20
Total maintainers: 1

cran.r-project.org: pcadapt

Fast Principal Component Analysis for Outlier Detection

Homepage: https://github.com/bcm-uga/pcadapt
Documentation: http://cran.r-project.org/web/packages/pcadapt/pcadapt.pdf
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Latest release: 4.4.1
published 12 months ago

Versions: 20
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 968 Last month
Docker Downloads: 1,549

Rankings

Forks count: 6.8%

Stargazers count: 8.8%

Downloads: 13.3%

Average: 13.8%

Docker downloads count: 16.5%

Dependent packages count: 18.1%

Dependent repos count: 19.2%

Maintainers (1)

florian.prive.21@gmail.com

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

RSpectra * imports
Rcpp >= 0.12.8 imports
bigutilsr >= 0.3 imports
data.table * imports
ggplot2 * imports
magrittr * imports
mmapcharr >= 0.3 imports
plotly * suggests
shiny * suggests
spelling * suggests
testthat * suggests
vcfR * suggests

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

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite