COMBIA: Synergy/Antagonism Analyses of Drug Combinations

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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).

Author
Muhammad Kashif
Date of publication
2015-07-26 18:53:01
Maintainer
Muhammad Kashif <Muhammad.Kashif@medsci.uu.se>
License
GPL (>= 2)
Version
1.0-4

View on CRAN

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...

Files in this package

COMBIA
COMBIA/inst
COMBIA/inst/raw
COMBIA/inst/raw/optima.log
COMBIA/inst/raw/FluoOptima_384_2014-03-28test.xls
COMBIA/inst/raw/processedData.csv
COMBIA/inst/raw/testData.xls
COMBIA/inst/raw/rawDataPreProcessed.csv
COMBIA/inst/raw/FluoOptima_384_2014-03-28test.txt
COMBIA/NAMESPACE
COMBIA/R
COMBIA/R/COMBIA.R
COMBIA/MD5
COMBIA/DESCRIPTION
COMBIA/man
COMBIA/man/createUniquePertbs.Rd
COMBIA/man/synergySignificant.Rd
COMBIA/man/extractReplicateValues.Rd
COMBIA/man/extractKey.Rd
COMBIA/man/selectPlate.Rd
COMBIA/man/applyLoewe.Rd
COMBIA/man/synAntPlot.Rd
COMBIA/man/readFile.Rd
COMBIA/man/readMacSynergyValues.Rd
COMBIA/man/readFMCAValues.Rd
COMBIA/man/calculateSynergy.Rd
COMBIA/man/readOtherValues.Rd
COMBIA/man/removeOutliers.Rd
COMBIA/man/loeweModel.Rd
COMBIA/man/combineDataFromMultipleFiles.Rd
COMBIA/man/cVCal.Rd
COMBIA/man/extractValuesFromRange.Rd
COMBIA/man/readFluostarPlates.Rd
COMBIA/man/applyBliss.Rd