Other packages > Find by keyword >

polyRAD  

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
View on CRAN: Click here


Download and install polyRAD package within the R console
Install from CRAN:
install.packages("polyRAD")

Install from Github:
library("remotes")
install_github("cran/polyRAD")

Install by package version:
library("remotes")
install_version("polyRAD", "2.0.0")



Attach the package and use:
library("polyRAD")
Maintained by
Lindsay V. Clark
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-08-02
Latest Update: 2022-11-06
Description:
Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) , and the Hind/He statistic for marker filtering is described by Clark et al. (2022) . A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) .
How to cite:
Lindsay V. Clark (2018). polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. R package version 2.0.0, https://cran.r-project.org/web/packages/polyRAD. Accessed 03 Dec. 2024.
Previous versions and publish date:
0.5-0 (2018-08-02 17:30), 1.0 (2018-11-20 00:30), 1.1 (2019-06-04 22:00), 1.2 (2020-05-12 23:10), 1.3 (2021-01-06 08:30), 1.4 (2021-03-23 00:00), 1.5 (2021-09-03 00:20), 1.6 (2022-02-15 22:30)
Other packages that cited polyRAD R package
View polyRAD citation profile
Other R packages that polyRAD depends, imports, suggests or enhances
Complete documentation for polyRAD
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

telemac  
R Interface to the TELEMAC Model Suite
An R interface to the TELEMAC suite for modelling of free surface flow. This includes methods for m ...
Download / Learn more Package Citations See dependency  
donut  
Nearest Neighbour Search with Variables on a Torus
Finds the k nearest neighbours in a dataset of specified points, adding the option to wrap certain ...
Download / Learn more Package Citations See dependency  
CRANsearcher  
RStudio Addin for Searching Packages in CRAN Database Based on Keywords
One of the strengths of R is its vast package ecosystem. Indeed, R packages extend from visualizatio ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
FSInteract  
Fast Searches for Interactions
Performs fast detection of interactions in large-scale data using the method of random intersection ...
Download / Learn more Package Citations See dependency  
EDOtrans  
Euclidean Distance-Optimized Data Transformation
A data transformation method which takes into account the special property of scale non-invariance w ...
Download / Learn more Package Citations See dependency  

23,310

R Packages

200,798

Dependencies

63,203

Author Associations

23,278

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA