BaseIndexList-class     An S4 class to hold a list of indices, with the
                        possibility to specify the offset of the
                        indices. IndexList and SignedIndexList extend
                        this class
GmtList                 Convert a list to a GmtList object
GmtList-class           An S4 class to hold geneset in the GMT file in
                        a list, each item in the list is in in turn a
                        list containing following items: name, desc,
                        and genes.
IndexList               Convert a list to an IndexList object
IndexList-class         An S4 class to hold a list of integers as
                        indices, with the possibility to specify the
                        offset of the indices
SignedGenesets          Convert a list to a SignedGenesets object
SignedGenesets-class    An S4 class to hold signed genesets, each item
                        in the list is in in turn a list containing
                        following items: name, pos, and neg.
SignedIndexList         Convert a list into a SignedIndexList
SignedIndexList-class   An S4 class to hold a list of signed integers
                        as indices, with the possibility to specify the
                        offset of the indices
[.GmtList               Subsetting GmtList object into another GmtList
                        object
[[.GmtList              Subsetting GmtList object to fetch one gene-set
absLog10p               Absolute base-10 logarithm of p-values
appendGmtList           Append a GmtList object to another one
as.GmtList              Convert a list of gene symbols into a gmtlist
entropy                 Shannon entropy
entropyDiversity        Entropy-based sample diversity
entropySpecificity      Entropy-based gene-expression specificity
filterBySize            Filter a GmtList by size
filterPmat              Filter rows of p-value matrix under the
                        significance threshold
getLeadingEdgeIndexFromVector
                        Getting leading-edge indices from a vector
gini                    Calculate Gini Index of a numeric vector
gmtlist2signedGenesets
                        Convert gmtlist into a list of signed genesets
gsDesc                  Gene-set descriptions
gsGeneCount             Gene-set gene counts
gsGenes                 Gene-set member genes
gsName                  Gene-set names
gsNamespace             Gene-set namespaces
gsNamespace<-           gsNamespace<- is the synonym of setGsNamespace
hasNamespace            Whether namespace is set
isValidBaseIndexList    Function to validate a BaseIndexList object
isValidGmtList          Function to validate a GmtList object
isValidIndexList        Function to validate an IndexList object
isValidSignedGenesets   Function to validate a SignedGenesets object
isValidSignedIndexList
                        Function to validate a SignedIndexList object
matchGenes              Match genes in a list-like object to a vector
                        of genesymbols
offset                  Get offset from an IndexList object
offset<-                Set the offset of an 'IndexList' or a
                        'SignedIndexList' object
prettySigNames          Prettify default signature names
readCurrentSignatures   Load current BioQC signatures
readGmt                 Read in gene-sets from a GMT file
readSignedGmt           Read signed GMT files
sampleSpecialization    Entropy-based sample specialization
setDescAsNamespace      Set gene-set description as namespace
setNamespace            Set the namespace field in each gene-set within
                        a GmtList
show,GmtList-method     Show method for GmtList
show,IndexList-method   Show method for IndexList
show,SignedGenesets-method
                        Show method for SignedGenesets
show,SignedIndexList-method
                        Show method for SignedIndexList
simplifyMatrix          Simplify matrix in case of single row/columns
uniqGenesetsByNamespace
                        Make names of gene-sets unique by namespace,
                        and member genes of gene-sets unique
valTypes                prints the options of valTypes of wmwTest
wmwLeadingEdge          Identify BioQC leading-edge genes of one
                        gene-set
wmwTest                 Wilcoxon-Mann-Whitney rank sum test for
                        high-throughput expression profiling data
wmwTestInR              Wilcoxon-Mann-Whitney test in R
