COMBIA: Synergy/Antagonism Analyses of Drug Combinations
Version 1.0-4

A comprehensive synergy/antagonism analyses of drug combinations with quality graphics and data. The analyses can be performed by Bliss independence and Loewe additivity models. COMBIA provides improved statistical analysis and makes only very weak assumption of data variability while calculating bootstrap intervals (BIs). Finally, package saves analyzed data, 2D and 3D plots ready to use in research publications. COMBIA does not require manual data entry. Data can be directly input from wetlab experimental platforms for example fluostar, automated robots etc. One needs to call a single function only to perform all analysis (examples are provided with sample data).

AuthorMuhammad Kashif
Date of publication2015-07-26 18:53:01
MaintainerMuhammad Kashif <Muhammad.Kashif@medsci.uu.se>
LicenseGPL (>= 2)
Version1.0-4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("COMBIA")

Popular man pages

applyBliss: This function performs synergy analysis based on Bliss model...
applyLoewe: This function calculates Loewe synergy/antagonism and...
createUniquePertbs: Function to calculate possible unique perturbations of...
cVCal: The function calculates coefficient of variance (CV).
extractKey: Extracts the barcodes from a dataset, each experimental plate...
loeweModel: This function applies Loewe model.
readFluostarPlates: Read a file containing raw read outs and calculates survival...
See all...

All man pages Function index File listing

Man pages

applyBliss: This function performs synergy analysis based on Bliss model...
applyLoewe: This function calculates Loewe synergy/antagonism and...
calculateSynergy: Function calculates significant synergy/antagonism in...
combineDataFromMultipleFiles: It combines data from multiple files/experiments into a...
createUniquePertbs: Function to calculate possible unique perturbations of...
cVCal: The function calculates coefficient of variance (CV).
extractKey: Extracts the barcodes from a dataset, each experimental plate...
extractReplicateValues: On basis of input well ranges, the function extracts values...
extractValuesFromRange: Given a well/wells alphanumeric name e.g. "B2", this function...
loeweModel: This function applies Loewe model.
readFile: Read raw experimental data from a file. This function reads...
readFluostarPlates: Read a file containing raw read outs and calculates survival...
readFMCAValues: Read data from Fluorometric microculture cytotoxic assay...
readMacSynergyValues: Read data from macSynergyII format and clean for outliers.
readOtherValues: Read data from other than MacSynergy and FMCA format and...
removeOutliers: This function removes outliers from data. Outliers are...
selectPlate: Select one readout from the twice read data and store...
synAntPlot: This function prints and saves 2D and 3D plots of...
synergySignificant: Function "synergySignificant" calculates significant...

Functions

J Source code
Jmax Source code
applyBliss Man page Source code
applyLoewe Man page Source code
cVCal Man page Source code
calculateSiPredicted Source code
calculateSynergy Man page Source code
calculatesi Source code
combineDataFromMultipleFiles Man page Source code
createUniquePertbs Man page Source code
extractKey Man page Source code
extractReplicateValues Man page Source code
extractValuesFromRange Man page Source code
gradJ_a Source code
gradJ_h Source code
loeweModel Man page Source code
nlsComIntAct Source code
rangemean Source code
readFMCAValues Man page Source code
readFile Man page Source code
readFluostarPlates Man page Source code
readMacSynergyValues Man page Source code
readOtherValues Man page Source code
removeOutliers Man page Source code
selectPlate Man page Source code
startingGuessIC50nH Source code
synAntPlot Man page Source code
synergySignificant Man page Source code

Files

inst
inst/raw
inst/raw/optima.log
inst/raw/FluoOptima_384_2014-03-28test.xls
inst/raw/processedData.csv
inst/raw/testData.xls
inst/raw/rawDataPreProcessed.csv
inst/raw/FluoOptima_384_2014-03-28test.txt
NAMESPACE
R
R/COMBIA.R
MD5
DESCRIPTION
man
man/createUniquePertbs.Rd
man/synergySignificant.Rd
man/extractReplicateValues.Rd
man/extractKey.Rd
man/selectPlate.Rd
man/applyLoewe.Rd
man/synAntPlot.Rd
man/readFile.Rd
man/readMacSynergyValues.Rd
man/readFMCAValues.Rd
man/calculateSynergy.Rd
man/readOtherValues.Rd
man/removeOutliers.Rd
man/loeweModel.Rd
man/combineDataFromMultipleFiles.Rd
man/cVCal.Rd
man/extractValuesFromRange.Rd
man/readFluostarPlates.Rd
man/applyBliss.Rd
COMBIA documentation built on May 19, 2017, 6:10 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.