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.

Install the latest version of this package by entering the following in R:
install.packages("timma")
AuthorLiye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Bioconductor views Software StatisticalMethod
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

Functions

binarizeDrugTargets Man page
binarySet Man page
ci Man page
davis Man page
dec2bin Man page
drawGraph Man page
drugRank Man page
findSameCol Man page
findSameSet Man page
floating2 Man page
getBinary Man page
getBinary1 Man page
graycode2 Man page
graycode3 Man page
graycodeNames Man page
grays Man page
kiba Man page
maxcpp Man page
maxcpp1 Man page
miller_drug_response Man page
miller_drugs Man page
miller_interaction_binary Man page
miller_sensitivity Man page
miller_targets Man page
mincpp Man page
mincpp1 Man page
normalizeSensitivity Man page
searchSpace Man page
sffs Man page
sffsBinary Man page
sffsBinary1 Man page
sffsBinary2 Man page
sffsCategory Man page
sffsCategory1 Man page
sffsCategoryWeighted Man page
sffsCategoryWeighted1 Man page
sumcpp Man page
sumcpp1 Man page
targetRank Man page
timma Man page
TIMMA Man page
timmaBinary Man page
timmaBinary1 Man page
timmaCategory Man page
timmaCategory1 Man page
timmaCategoryWeighted Man page
timmaCategoryWeighted1 Man page
timmaModel Man page
timmaModel1 Man page
timma-package Man page
timmaSearchBinary Man page
timmaSearchBinary1 Man page
tyner_interaction_binary Man page
tyner_interaction_multiclass Man page
tyner_sensitivity Man page

Files

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

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