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sybil (version 1.0.2)

SyBiL - Efficient constrained based modelling in R

Description

The package SyBiL is a Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), linera MOMA, robustness analysis and flux variability analysis).

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Version

Install

install.packages('sybil')

Monthly Downloads

62

Version

1.0.2

License

GPL-3

Maintainer

Gabriel Gelius-Dietrich

Last Published

April 20th, 2012

Functions in sybil (1.0.2)

optsol_doublegenedel-class

Class "optsol_doublegenedel"
multiDel

Parallel (Multicore) Support for SyBiL
optObj_lpSolveAPI-class

Class "optObj_lpSolveAPI"
doubleGeneDel

Double Gene Deletion Experiment
optObj_cplex-class

Class "optObj_cplex"
optsol_doublefluxdel-class

Class "optsol_doublefluxdel"
findExchReact

Find Exchange Reactions
onlyChangeGPR

Change the GPR Rules
geneDeletion

Simulate N Gene Deletion Experiments
checksol-class

Structure of the Class "checksol"
optObj_clp-class

Class "optObj_clp"
optsol_blockedReact-class

Class "optsol_blockedReact"
changeGPR

Check and Change the GPR Rules
fluxVar

Flux Variability Analysis
optimizer

Performs Optimizations for the Gene/Flux Deletion Experiments
mod2irrev

Produces a Model in Irreversible Format
robAna

Robustness Analysis
SYBIL_SETTINGS

Set and Get SyBiL Parameters
checkReactId

Check if a Reaction Id is Valid
optsol_robAna-class

Class "optsol_robAna"
doubleReact

Identifies Identical Reactions
ypd

In Sillico YPD Medium
checkOptSol

Interprets an Object of Class Optsol
changeObjFunc

Sets/changes the Objective Function
sybilError-class

Class "sybilError"
optsol_genedel-class

Class "optsol_genedel"
checkDefaultMethod

Validate Solver and Method
sybilLog-class

Class "sybilLog"
optsol-class

Class optsol
prepProbObj

Creates an Instance of Class "optObj"
Ec_core

Escherichia coli Core Metabolic Model
optsol_simpleFBA-class

Class "optsol_simpleFBA"
modelorg2tsv

Write an Instance of Class modelorg to File
optsol_fluxdel-class

Class "optsol_fluxdel"
optsol_fluxVar-class

Class "optsol_fluxVar"
ppProc-class

Class "ppProc"
optObj-class

Strukture of Class "optObj"
oneFluxDel

One Flux Deletion Experiment
reactId-class

Strukture of Class "reactId"
doubleFluxDel

Double Flux Deletion Experiment
rmReact

Remove Reactions From a Model
readTSVmod

Read a Metabolic Network in a TSV (CSV) Format
oneGeneDel

One Gene Deletion Experiment
sybil-package

SyBiL -- Systems Biology Library
blockedReact

Find Blocked Reactions in a Metabolic Network
sybilStack

A Data Type Providing Stack And Queue Functionality
simpleFBA

Flux Balance Analysis with a Given Model
fluxDistribution-class

Class "fluxDistribution"
changeBounds

Change Variable Bounds in a Metabolic Network
onlyCheckGPR

Check the GPR Rules
geneDel

Get Gene-Reaction Association
modelorg_irrev-class

Class for Metabolic Networks in Irreversible Format.
sybil-internal

Internal SyBiL Functions
optObj_glpk-class

Class "optObj_glpk"
addReact

Add/Change Reactions in a Model
addExchReact

Add Exchange Reactions to a Model
modelorg-class

Strukture of Class "modelorg"
printObjFunc

Prints a Human Readable Objective Function