balanced.cv.folds       Create balanced folds for cross validation
balanced.cv.folds.from.vector
                        Create balanced folds for cross validation
balanced.train.and.test
                        Get a balanced test and train dataset
balanced.train.and.test.from.vector
                        Get a balanced test and train dataset
base.dir                change base.dir for run.cache
build.function.digest   Build digest of function from the actual code
cache.compression       change cache.compression for run.cache
calculate.result        Calculate/load result and save if necessary
ccds.genes.internal     Download coding genes from CCDS
coding.genes            Retrive coding genes from known databases
coding.genes.ensembl    Ensembl coding genes, local function
create.directory.for.cache
                        Create directories for cache
curl.workaround         Workaround for bug with curl when fetching
                        specific ensembl mirror
digest.cache            Default digest method
draw.cov.matrix         Plot covariance heatmap from matrix
gen.synth.xdata         Generate xdata matrix with pre-determined
                        covariance
getBM.internal          Internal call to biomaRt::getBM
getHsapiensMart.internal
                        Get hsapiens mart from biomaRt
join.ensembl.and.ccds   Join genes from ensembl and ccds in a single
                        table
listEnsemblMirrors      Internal function to list mirrors
loose.rock              loose.rock: compilation of data science
                        functions
loose.rock.options      Constants for 'loose.rock' package
multiplot               Multiple plot
my.colors               Custom pallete of colors
my.symbols              Custom pallete of symbols in plots
proper                  Capitalizes all words in string
release_questions       Questions to ask when calling
                        devtools::release()
run.cache               Run function and save cache
run.cache,function-method
                        Run function and save cache
save.run.cache          Saving the cache
search.genes.internal   Search genes in biomaRt
show.message            Show messages option in run.cache
tempdir.cache           Temporary directory for runCache
write.readme            Write a file in run-cache directory to explain
                        the origin
