SimRAD: Simulations to Predict the Number of RAD and GBS Loci
Version 0.96

Provides a number of functions to simulate restriction enzyme digestion, library construction and fragments size selection to predict the number of loci expected from most of the Restriction site Associated DNA (RAD) and Genotyping By Sequencing (GBS) approaches. SimRAD estimates the number of loci expected from a particular genome depending on the protocol type and parameters allowing to assess feasibility, multiplexing capacity and the amount of sequencing required.

Browse man pages Browse package API and functions Browse package files

AuthorOlivier Lepais [aut, cre], Jason Weir [aut]
Date of publication2016-01-06 17:22:25
MaintainerOlivier Lepais <olepais@st-pee.inra.fr>
LicenseGPL-2
Version0.96
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SimRAD")

Man pages

adapt.select: Function to select fragments according to the flanking...
exclude.seqsite: Function to exclude fragments containing a specified...
insilico.digest: Function to digest DNA sequence using one or two restriction...
insilico.digest.internal: Internal function to digest DNA sequence using one...
ref.DNAseq: Function to import a reference DNA sequence from a Fasta...
sim.DNAseq: Function to simulate randomly generated DNA sequence.
SimRAD-package: Simulations to predict the number of loci expected in RAD and...
size.select: Function to select fragments according to their size.

Functions

SimRAD Man page
SimRAD-package Man page
adapt.select Man page Source code
exclude.seqsite Man page Source code
insilico.digest Man page Source code
insilico.digest.internal Man page Source code
ref.DNAseq Man page Source code
sim.DNAseq Man page Source code
size.select Man page Source code

Files

NAMESPACE
R
R/ref.DNAseq.R
R/insilico.digest.R
R/adapt.select.R
R/exclude.seqsite.R
R/size.select.R
R/insilico.digest.internal.R
R/sim.DNAseq.R
MD5
DESCRIPTION
man
man/insilico.digest.Rd
man/adapt.select.Rd
man/sim.DNAseq.Rd
man/exclude.seqsite.Rd
man/ref.DNAseq.Rd
man/SimRAD-package.Rd
man/size.select.Rd
man/insilico.digest.internal.Rd
SimRAD documentation built on May 19, 2017, 10:54 a.m.