timma: Target Inhibition Interaction using Maximization and Minimization Averaging

Prediction and ranking of drug combinations based on their drug-target interaction profiles and single-drug sensitivities in a given cancer cell line or patient-derived sample.

Author
Liye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Date of publication
2015-02-28 12:17:41
Maintainer
Jing Tang <jing.tang@helsinki.fi>
License
Artistic License 2.0
Version
1.2.1

View on CRAN

Man pages

binarizeDrugTargets
Binarize the drug target profile data
binarySet
Search for supersets and subsets
ci
The combination index extracted from Figure 1B of the Miller...
davis
Drug-target profile for 72 drugs and 442 targets.
dec2bin
Convert decimal values to binary values
drawGraph
Draw graph function
drugRank
Generate the list of ranked drug combinations
findSameCol
Find the same column from a matrix
findSameSet
Find the same columns from two matrices
floating2
Filter targets
getBinary
Binary set for multiclass data
getBinary1
Weighted binary set for multiclass data
graycode2
Graycode Function
graycode3
Gray code function for matrix indexes
graycodeNames
Names for the predicted sensitivity matrix
grays
Generate gray code
kiba
Kiba interaction data
maxcpp
Search for the max values of 3D matrix in cpp
maxcpp1
Search for the max values of 2D matrix in cpp
miller_drug_response
The single drug does-response data from the Miller study
miller_drugs
A drug list from Miller study
miller_interaction_binary
The binarized drug-target data for the Miller drugs
miller_sensitivity
The scaled drug sensitivity data for the Miller drugs
miller_targets
The curated drug-target data for the Miller drugs
mincpp
Search for the min values of 3D matrix in cpp
mincpp1
Search for the min values of 2D matrix in cpp
normalizeSensitivity
Normalize the drug sensitivity data
searchSpace
Generate search space
sffs
SFFS switch function
sffsBinary
Model selection with sffs for the binary drug-target...
sffsBinary1
Model selection with sffs for the binary drug-target...
sffsBinary2
Model selection with filtered binary drug-target interaction...
sffsCategory
Model selection with sffs for the multi-class drug-target...
sffsCategory1
Model selection with sffs for the multi-class drug-target...
sffsCategoryWeighted
Model selection with sffs for the multi-class drug-target...
sffsCategoryWeighted1
Model selection with sffs for the multi-class drug-target...
sumcpp
Sum for 3D matrix
sumcpp1
Sum for 2D matrix in cpp
targetRank
Generate the list of ranked target combinations
timma
Main function for the timma package
timmaBinary
Predicting drug sensitivity with binary drug-target...
timmaBinary1
Predicting drug sensitivity with binary drug-target...
timmaCategory
Predicting drug sensitivity with multi-class drug-target...
timmaCategory1
Predicting drug sensitivity with multi-class drug-target...
timmaCategoryWeighted
Predicting drug sensitivity with multi-class drug-target...
timmaCategoryWeighted1
Predicting drug sensitivity with multi-class drug-target...
timmaModel
Predicting drug sensitivity with binary drug-target...
timmaModel1
Predicting drug sensitivity with binary drug-target...
timma-package
Target Inhibition inference using Maximization and...
timmaSearchBinary
Prediction in the search space with one.sided TIMMA model
timmaSearchBinary1
Prediction in the search space with two.sided TIMMA model
tyner_interaction_binary
A binary drug-target interaction data
tyner_interaction_multiclass
A multi-class drug-target interaction data
tyner_sensitivity
The drug sensitivity data

Files in this package

timma
timma/inst
timma/inst/doc
timma/inst/doc/timma.pdf.asis
timma/inst/doc/timma.pdf
timma/src
timma/src/Makevars
timma/src/max_min.cpp
timma/src/Makevars.win
timma/src/RcppExports.cpp
timma/NAMESPACE
timma/data
timma/data/miller_drug_response.rda
timma/data/kiba.rda
timma/data/tyner_interaction_binary.rda
timma/data/miller_sensitivity.rda
timma/data/miller_drugs.rda
timma/data/davis.rda
timma/data/tyner_interaction_multiclass.rda
timma/data/datalist
timma/data/ci.rda
timma/data/miller_interaction_binary.rda
timma/data/tyner_sensitivity.rda
timma/R
timma/R/tyner_interaction_binary.R
timma/R/tyner_interaction_multiclass.R
timma/R/getBinary1.R
timma/R/miller_targets.R
timma/R/kiba.R
timma/R/timmaCategoryWeighted1.R
timma/R/timmaSearchBinary.R
timma/R/floating2.R
timma/R/timmaModel1.R
timma/R/graycodeNames.R
timma/R/timma.R
timma/R/timmaCategoryWeighted.R
timma/R/binarySet.R
timma/R/getBinary.R
timma/R/timmaCategory1.R
timma/R/sffsCategory1.R
timma/R/drugRank.R
timma/R/miller_interaction_binary.R
timma/R/sffs.R
timma/R/binarizeDrugTargets.R
timma/R/sffsBinary2.R
timma/R/sffsCategory.R
timma/R/graycode3.R
timma/R/drawGraph.R
timma/R/graycode2.R
timma/R/grays.R
timma/R/findSameSet.R
timma/R/RcppExports.R
timma/R/searchSpace.R
timma/R/davis.R
timma/R/timmaCategory.R
timma/R/sffsBinary1.R
timma/R/normalizeSensitivity.R
timma/R/timmaBinary.R
timma/R/timmaSearchBinary1.R
timma/R/sffsCategoryWeighted.R
timma/R/findSameCol.R
timma/R/timmaModel.R
timma/R/tyner_sensitivity.R
timma/R/dec2bin.R
timma/R/targetRank.R
timma/R/miller_sensitivity.R
timma/R/sffsCategoryWeighted1.R
timma/R/timmaBinary1.R
timma/R/ci.R
timma/R/sffsBinary.R
timma/R/miller_drugs.R
timma/R/miller_drug_response.R
timma/vignettes
timma/vignettes/timma.pdf.asis
timma/MD5
timma/build
timma/build/vignette.rds
timma/DESCRIPTION
timma/man
timma/man/timmaCategory1.Rd
timma/man/tyner_interaction_binary.Rd
timma/man/timmaSearchBinary1.Rd
timma/man/ci.Rd
timma/man/miller_drug_response.Rd
timma/man/timmaCategoryWeighted.Rd
timma/man/miller_interaction_binary.Rd
timma/man/tyner_interaction_multiclass.Rd
timma/man/timmaModel1.Rd
timma/man/sumcpp1.Rd
timma/man/tyner_sensitivity.Rd
timma/man/findSameSet.Rd
timma/man/binarizeDrugTargets.Rd
timma/man/sffsBinary2.Rd
timma/man/drugRank.Rd
timma/man/binarySet.Rd
timma/man/findSameCol.Rd
timma/man/getBinary.Rd
timma/man/timmaCategory.Rd
timma/man/graycode2.Rd
timma/man/sffsBinary.Rd
timma/man/searchSpace.Rd
timma/man/maxcpp1.Rd
timma/man/normalizeSensitivity.Rd
timma/man/timmaBinary.Rd
timma/man/floating2.Rd
timma/man/drawGraph.Rd
timma/man/miller_drugs.Rd
timma/man/sffsBinary1.Rd
timma/man/timma-package.Rd
timma/man/miller_sensitivity.Rd
timma/man/sffsCategoryWeighted.Rd
timma/man/dec2bin.Rd
timma/man/timmaSearchBinary.Rd
timma/man/maxcpp.Rd
timma/man/targetRank.Rd
timma/man/sffsCategory.Rd
timma/man/sffsCategoryWeighted1.Rd
timma/man/sumcpp.Rd
timma/man/miller_targets.Rd
timma/man/timma.Rd
timma/man/mincpp.Rd
timma/man/mincpp1.Rd
timma/man/graycode3.Rd
timma/man/getBinary1.Rd
timma/man/sffs.Rd
timma/man/kiba.Rd
timma/man/timmaBinary1.Rd
timma/man/sffsCategory1.Rd
timma/man/graycodeNames.Rd
timma/man/timmaCategoryWeighted1.Rd
timma/man/grays.Rd
timma/man/davis.Rd
timma/man/timmaModel.Rd