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R language bioinformatics analysis package wrapper for VisualBasic
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Bioconductor rollback repository Mar 9, 2019
RDotNET.Extensions.GCModeller config projects Nov 13, 2018
RDotNET.Extensions.VisualBasic improvements for write csv handler Apr 17, 2019
RDotNET config projects Nov 13, 2018
RDotNet.Extensions.Bioinformatics rollback repository Mar 9, 2019
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R.GCModellerExtensions.sln
README.md
README.txt
_config.yml
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README.md

R.Bioinformatics

R language bioinformatics analysis package wrapper for VisualBasic.

This project is aim at provides a high performance distribution and parallel computing environment for bioinformatics data analysis of VisualBasic hybrid programming with R.

Runtime

Require of sciBASIC# computing runtime

PM> Install-Package sciBASIC

Or reference to source code project:

https://github.com/xieguigang/sciBASIC#

Introduction

Folks from project: R.NET https://rdotnet.codeplex.com/

Currently there is a bioconductor GUI installer was included in this project for those beginners in the area of bioinformatics and some of the common used R package wrapper class which written in VisualBasic was developed to extends the biological data analysis ability of GCModeller and Microsoft .NET languages.

VisualBasic & R language hybrids

For example:

Imports RDotNET.Extensions.VisualBasic
Imports RDotNET.Extensions.VisualBasic.API.base
Imports RDotNET.Extensions.VisualBasic.API.utils
Imports RDotNET.Extensions.Bioinformatics.deSolve.API
Imports RDotNET.Extensions.Bioinformatics.deSolve

' Entering Microsoft R language environment by using VisualBasic language syntax specific
' Enable R session runtime
SyncLock R
    With R

        ' Setup variables in R language from VisualBasic
        .call = $"p      <- {p}"
        .call = $"beta   <- {beta}"
        .call = $"c      <- {c}"
        .call = $"delta  <- {delta}"
        .call = $"U0     <- {U0}"
        .call = $"rho    <- {rho}"
        .call = $"lambda <- {lambda}"

        ' For variable initialize like: p <- value
        ' Dim p As var = value, this expression is also working
    End With
End SyncLock

' The initial value for infected cells(I0) is set to zero.
' The best model based on the Akaike Information Criterion(AIC) is presented in Figure3, providing an estimate of 9 ffu/ml for V0.
' The initial number of susceptible cells(U0) can be taken from the experiment in Half mannetal. (2008) as 5 × 10^5.
Dim yini = "c(U=U0, I=0, V=9)"
Dim model = [function](
    {
        "t",
        "y",
        "params"
    },
_
    "with(as.list(y), {

        dU <- lambda - rho * U - beta * U * V
        dI <- beta * U * V - delta * I
        dV <- p * I - c * V

        list(c(dU, dI, dV))
})")

require("deSolve")

' Calling ode{deSolve}
Dim times = seq([from]:=0, [to]:=5.6, by:=0.01)
Dim out = ode(y:=yini,
              times:=times,
              func:=model,
              parms:=NULL,
              method:=integrator.rk4)

' Calling write.csv{utils}
Call write.csv(out, "x:\ebola_test.csv")
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