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easyRNASeq (version 2.8.2)

Count summarization and normalization for RNA-Seq data

Description

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

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Version

Version

2.8.2

License

Artistic-2.0

Maintainer

Nicolas Delhomme

Last Published

February 15th, 2017

Functions in easyRNASeq (2.8.2)

BamParam class

Class "BamParam"
easyRNASeq BamParam constructor

BamParam constructor
easyRNASeq AnnotParam accessors

Accessors for AnnotParam class
easyRNASeq-datasets

Dataset included in the package
easyRNASeq coverage methods

Compute the coverage from a Short Read Alignment file
Deprecated functions

The following function have been deprecated:
file.exists methods

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
RNAseq class

Class "RNAseq"
easyRNASeq BamParam accessors

Accessors for BamParam class
getBamFileList

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
easyRNASeq package

Count summarization and normalization pipeline for Next Generation Sequencing data.
easyRNASeq RnaSeqParam accessors

Accessors for RnaSeqParam class
easyRNASeq accessors

Accessors for RNAseq class
RnaSeqParam 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
validate,BamFile-method

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
AnnotParam class

Class "AnnotParam"
ShortRead additional methods

Methods extending the ShortRead package functionalities
Defunct functions

The following function are defunct:
  • fetchAnnotation
  • knownOrganisms
  • plotDispersionEstimates,DGEList-method
AnnotParam internal methods

Internal methods of AnnotParam objects
DESeq additional methods

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
basename methods

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
show methods

Display the content of classes from the easyRNASeq package.
genomeIntervals additional methods

Extension for the genomeIntervals package
print methods

Pretty print the content of classes from the easyRNASeq package.
easyRNASeq RnaSeqParam constructor

RnaSeqParam constructor
edgeR additional methods

Extension for the edgeR package