pooledpeaks
pooledpeaks: Open-Source Fragment Scoring and Analysis Workflow for Population Genetic Analyses of Microsatellite Markers in Pooled Samples - Published in JOSS (2025)
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Published in Journal of Open Source Software
Scientific Fields
Repository
The Pooled Peaks Package Developed by the Blanton Lab as part of Kathleen Kuesters' Dissertation
Basic Info
- Host: GitHub
- Owner: kmkuesters
- License: gpl-3.0
- Language: HTML
- Default Branch: master
- Size: 1.91 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 4
Metadata Files
README.md
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Package Overview
pooledpeaks is designed for analyzing genetic data obtained from Fragment
Analysis output files (.fsa) of pooled biological samples. It provides functions
for a comprehensive analysis pipeline from processing .fsa files, to cleaning
the peak data, and conducting population genetic analyses. Some features are
listed below and a usage example of the entire pipeline is included as a vignette.
Please check out the Contributing Guidelines for
information on how to add to this package.
Installation Instructions
You can install the package directly from GitHub using the following instructions:
Open R and copy the following code into your console
Install devtools and pooledpeaks from GitHub
r
install.packages("devtools")
devtools::install_github("kmkuesters/pooledpeaks")
Install pooledpeaks directly from CRAN
r
install.packages("pooledpeaks")
Features
For a detailed example of how to apply the functions contained in this package
please see the Introduction to Using the pooledpeaks
Workflow.
Example data can be found on GitHub under the inst/extdata folder including .fsa
files and a formatted "Multiplex_frequencies.txt" file for the Genetic Analysis
portion.
- Peak Scoring: Process
.fsafiles and score peaks contained therein.
r
check_fsa_v_batch()
fsa_metadata()
fsa_batch_imp()
associate_dyes()
score_markers_rev3()
- Data Manipulation: Clean and prepare peak data for downstream analyses.
r
clean_scores()
lf_to_tdf()
data_manipulation()
Rep_check()
PCDM()
LoadData()
Population Genetics Analysis:
- Calculate Gene Identity Matrix and Genetic Distance Matrix
- Calculate diversity indices
- Calculate differentiation indices
- Perform cluster analysis
r
TypedLoci()
GeneIdentityMatrix()
GeneticDistanceMatrix()
GST()
JostD()
cluster()
- Visualization: Visualize the peak scoring and genetic analysis results.
r
MDSplot()
Sample Data
The sample .fsa files included in this package are provided for demonstration
purposes and originate from two sources:
- Schistosoma haematobium laboratory isolates, used for preliminary testing
of the
pooledpeaksworkflow. These data contain no identifiable or human subject information. - De-identified Schistosoma mansoni samples from a three studies conducted in Brazil, extracted from discarded human waste. These files were originally used for genetic analysis and are shared here in anonymized form to illustrate compatibility with additional species and data sources.These studies are described in detail by Long et al. (2022), available at https://www.nature.com/articles/s41598-022-04776-0:
These files are intended solely to demonstrate the functionality of the
pooledpeaks package and are not for diagnostic or clinical use.To access the
example .fsa files included with the package, use the following path within R:
r
system.file("extdata", package = "pooledpeaks")
The pooledpeaks package was developed by the Blanton Lab as part of Kathleen Kuesters' dissertation.
References:
- Covarrubias-Pazaran et al. (2016) doi:10.1186/s12863-016-0365-6
- Long et al. (2022) doi:10.1038/s41598-022-04776-0
- Jost (2008) doi:10.1111/j.1365-294x.2008.03887.x
- Nei (1973) doi:10.1073/pnas.70.12.3321
- Foulley et al. (2006) doi:10.1016/j.livprodsci.2005.10.021
- Chao et al. (2008) doi:10.1111/j.1541-0420.2008.01010.x
Owner
- Login: kmkuesters
- Kind: user
- Repositories: 1
- Profile: https://github.com/kmkuesters
JOSS Publication
pooledpeaks: Open-Source Fragment Scoring and Analysis Workflow for Population Genetic Analyses of Microsatellite Markers in Pooled Samples
Authors
Department of Tropical Medicine and Infectious Disease, Tulane University Celia Scott Weatherhead School of Public Health and Tropical Medicine, New Orleans, LA 70112, United States of America
Department of Tropical Medicine and Infectious Disease, Tulane University Celia Scott Weatherhead School of Public Health and Tropical Medicine, New Orleans, LA 70112, United States of America
Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States of America, Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America
Independent Researcher, United States of America
Bahiana School of Medicine and Public Health, Av. Silveira Martins, n 3386, Salvador, Bahia, 41150-100, Brazil, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Candeal, CEP 40296-710, Salvador, Bahia, Brazil
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Candeal, CEP 40296-710, Salvador, Bahia, Brazil
Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Candeal, CEP 40296-710, Salvador, Bahia, Brazil, Faculdade de Medicina, Universidade Federal da Bahia, Praça XV de novembro, s/n - Largo do Terreiro de Jesus, CEP 40026-010, Salvador, Bahia, Brazil, Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, Connecticut, 06510, United States of America
Department of Tropical Medicine and Infectious Disease, Tulane University Celia Scott Weatherhead School of Public Health and Tropical Medicine, New Orleans, LA 70112, United States of America
Editor
Charlotte Soneson
Tags
population genetics fragment analysis pooled samples .fsaGitHub Events
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Last synced: 6 months ago
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Top Authors
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Packages
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Total downloads:
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- Total versions: 8
- Total maintainers: 1
cran.r-project.org: pooledpeaks
Genetic Analysis of Pooled Samples
- Homepage: https://github.com/kmkuesters/pooledpeaks
- Documentation: http://cran.r-project.org/web/packages/pooledpeaks/pooledpeaks.pdf
- License: GPL (≥ 3)
-
Latest release: 1.2.2
published 10 months ago