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.

AuthorLiye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Date of publication2015-02-28 12:17:41
MaintainerJing Tang <jing.tang@helsinki.fi>
LicenseArtistic License 2.0
Version1.2.1

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

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