SpliceCountSet-class    Class '"SpliceCountSet"'
[-methods               Methods for Function '['.
aaGapSites-class        Class '"aaGapSites"'
addGeneAligns           Reads a bamRange object for a given
                        'bamReader', 'refGenome' and gene name.
addGenomeData           Add MaxEnt-scores, Exon-Intron junction
                        sequences score to Feature Data in
                        'ExpressionSet' object.
addGenomeData,gapSites,DNAStringSet,refJunctions-method
                        Add MaxEnt-scores, Exon-Intron junction
                        sequences score to Feature Data in 'gapSites'
                        object.
addHbond                Class '"hbond"': Provides data and functions
                        for calculation of HBond scores for 5'
                        splice-sites.
addMaxEnt               addMaxEnt: Extract subset of data contained in
                        given range given object.
alt_left_ranks          alt_left_ranks and alt_right_ranks functions:
                        Identification of alternative splicing events
                        from gapped alignments.
annGapSites-class       Class '"annGapSites"'
annotate,ExpressionSet,refJunctions-method
                        Adds annotation data to existing ExpressionSet
                        (created by 'readExpSet')
annotation              Annotation functions for 'gapSites' objects
as.data.frame-methods   'as.data.frame' Returning content of
                        data.frame.
c-methods               Coercing functions 'c'.
cRanges-class           Class '"cRanges"': Centered ranges.
caRanges-class          Class '"caRanges"'
cdRanges-class          Class '"cdRanges"'
countByGeneName         Reads align number for selected gene from
                        multiple BAM-files.
dim-methods             'dim': Return dimensions of contained
                        data.frame.
dnaGapSites-class       Class '"dnaGapSites"'
dnaRanges               Reads a bamRange object for a given
                        'bamReader', 'refGenome' and gene name.
extractByGeneName       extractByGeneName: Extract subset for sites
                        which lie in range(s) defined by given gene
                        list.
extractRange            extractRange: Extract subset from object where
                        records lie in given range.
gapSites                Creating 'gapSites' and 'dnaGapSites' objects.
gapSites-class          Class '"gapSites"': Container for tabulated
                        alignment gap positions on RNA-seq data.
getGapSites             Read 'gapSites'
hbond-class             Class '"hbond"'
head-methods            'head' Return first lines of contained
                        data.frame.
initialize-methods      'initialize' Initializing objects.
keyProfiler-class       Class '"keyProfiler"'
lCodons                 xCodon methods
lJunc                   xJunc methods: lJunc, rJunc, lrJunc
lJuncStrand             xJuncStrand methods: lJuncStrand, rJuncStrand,
                        lrJuncStrand
lrCodons                lrCodon methods
maxEnt-class            Class '"maxEnt"'
merge-methods           'merge' Merging two objects into one.
plotGeneAlignDepth      plotGeneAlignDepth: Plots of read alignment
                        depth for genetic regions
rangeByGeneName         Reads a bamRange object for a given
                        'bamReader', 'refGenome' and gene name.
readCuffGeneFpkm        Reads FPKM values into ExpressionSet.
readExpSet              Reads align number or gptm or rpmg value from
                        all given BAM-files and all identified align
                        gaps into ExpressionSet.
readMergedBamGaps       Reads an object of type 'gapSites' using a
                        vector of BAM file names.
readTabledBamGaps       readTabledBamGaps function
seqlogo                 seqlogo: Plotting sequence logo for 'cdRanges'
                        and 'dnaGapSites' objects.
silic_tryp              silic_tryp function
sortTable-methods       Sorting contained data with 'sortTable'.
spliceSites-package     Calculate information on splice-sites from
                        gapped alignments in RNA-seq data.
trim_left               trim and resize methods: trim_left, trim_right,
                        resize_left, resize_right
truncateSeq             truncateSeq method
truncate_seq            truncate_seq function
trypsinCleave           trypsinCleave method
uniqueJuncAnn           uniqueJuncAnn method for ExpressionSet
write.files             write.files
