AnnotParam class        Class "AnnotParam"
BamParam class          Class "BamParam"
BiocFileCache methods   Manages the data necessary for the examples
                        using BiocFileCache
DESeq additional methods
                        Extension for the DESeq package
Defunct functions       The following function are defunct: 
                        'easyRNASeq'  'fetchCoverage' 
                        'fetchAnnotation'  'knownOrganisms' 
                        'plotDispersionEstimates,DGEList-method'
IRanges additional methods
                        Extension of the IRanges package
RNAseq class            Class "RNAseq"
RnaSeqParam class       Class "RnaSeqParam"
ShortRead additional methods
                        Methods extending the ShortRead package
                        functionalities
basename methods        Extend the basename function to display
                        Rsamtools BamFile class basename
createSyntheticTranscripts,AnnotParamCharacter-method
                        Methods to create synthetic transcripts
easyRNASeq AnnotParam accessors
                        Accessors for AnnotParam class
easyRNASeq AnnotParam constructor
                        AnnotParam constructor
easyRNASeq BamParam accessors
                        Accessors for BamParam class
easyRNASeq BamParam constructor
                        BamParam constructor
easyRNASeq GenomicRanges package extension
                        Extension of the GenomicRanges package
easyRNASeq RnaSeqParam accessors
                        Accessors for RnaSeqParam class
easyRNASeq RnaSeqParam constructor
                        RnaSeqParam constructor
easyRNASeq accessors    Accessors for RNAseq class
easyRNASeq annotation methods
                        Get genic annotation from a gff3/gtf file or
                        using biomaRt
easyRNASeq correction methods
                        easyRNASeq count table correction to RPKM
easyRNASeq coverage methods
                        Compute the coverage from a Short Read
                        Alignment file
easyRNASeq defunct annotation methods
                        Defunct annotation function
easyRNASeq island methods
                        Identify expressed regions de-novo
easyRNASeq package      Count summarization and normalization pipeline
                        for Next Generation Sequencing data.
easyRNASeq summarization methods
                        Count methods for RNAseq object
easyRNASeq,character-method
                        easyRNASeq method
easyRNASeq-datasets     Dataset included in the package
edgeR additional methods
                        Extension for the edgeR package
file.exists methods     Extend the file.exists function to check the
                        path slot of a Rsamtools BamFile class for
                        existence
genomeIntervals additional methods
                        Extension for the genomeIntervals package
getBamFileList          Get a BamFileList from a list of filenames
parallel additional methods
                        parallel additional methods
print methods           Pretty print the content of classes from the
                        easyRNASeq package.
show methods            Display the content of classes from the
                        easyRNASeq package.
simpleRNASeq,BamFileList,RnaSeqParam-method
                        simpleRNASeq method
validate,BamFile-method
                        Extension of the Rsamtools package
