caret, randomForest, GenomicRanges, GenomeInfoDb,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, S4Vectors,
org.Hs.eg.db, rlang

Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for
prioritizing cancer driver genes using somatic genomics data. BMC
Bioinformatics <doi:10.1186/s12859-021-04203-7>.

caret, randomForest, GenomicRanges, GenomeInfoDb,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, S4Vectors, org.Hs.eg.db,
rlang,

Regression and association models for clustered categorical responses
Fit regression and association models for clustered categorical
responses using dependence ratio as a measure of association

Regression and association models for repeated categorical data
Likelihood-based marginal regression and association modelling for repeated, or otherwise clustered, categorical responses using dependence ratio as a measure of the association

Likelihood-based marginal regression and association
modelling for repeated, or otherwise clustered, categorical
responses using dependence ratio as a measure of the
association