Class "BamParam"
easyRNASeq BamParam constructor
BamParam constructor
easyRNASeq AnnotParam accessors
Accessors for AnnotParam class
Dataset included in the package
easyRNASeq coverage methods
Compute the coverage from a Short Read Alignment file
The following function have been deprecated:
Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence
IRanges additional methods
Extension of the IRanges package
Class "RNAseq"
easyRNASeq BamParam accessors
Accessors for BamParam class
Get a BamFileList from a list of filenames
easyRNASeq island methods
Identify expressed regions de-novo
simpleRNASeq,BamFileList,RnaSeqParam-method
simpleRNASeq method
easyRNASeq summarization internal methods
Internal count and summarization methods
parallel additional methods
parallel additional methods
Count summarization and normalization pipeline for Next Generation Sequencing data.
easyRNASeq RnaSeqParam accessors
Accessors for RnaSeqParam class
Accessors for RNAseq class
Class "RnaSeqParam"
easyRNASeq,character-method
easyRNASeq method
easyRNASeq-global-variables
Objects created when the package is attached.
easyRNASeq internal methods
Internal methods of RNAseq objects
easyRNASeq summarization methods
Count methods for RNAseq object
Extension of the Rsamtools package
easyRNASeq annotation methods
Get genic annotation from a gff3/gtf file or using biomaRt
easyRNASeq GenomicRanges package extension
Extension of the GenomicRanges package
Class "AnnotParam"
ShortRead additional methods
Methods extending the ShortRead package functionalities
The following function are defunct:
fetchAnnotationknownOrganismsplotDispersionEstimates,DGEList-method AnnotParam internal methods
Internal methods of AnnotParam objects
Extension for the DESeq package
easyRNASeq annotation internal methods
Internal easyRNASeq annotation methods
easyRNASeq correction methods
easyRNASeq count table correction to RPKM
easyRNASeq AnnotParam constructor
AnnotParam constructor
Extend the basename function to display Rsamtools BamFile class basename
createSyntheticTranscripts,AnnotParamCharacter-method
Methods to create synthetic transcripts
easyRNASeq defunct annotation methods
Defunct annotation function
Display the content of classes from the easyRNASeq package.
genomeIntervals additional methods
Extension for the genomeIntervals package
Pretty print the content of classes from the easyRNASeq package.
easyRNASeq RnaSeqParam constructor
RnaSeqParam constructor
Extension for the edgeR package