
PACKAGE FEATURES

    o The Pasha package gives users access to alignedData class
    and associated methos which help to handle aligned reads from HTS
    sequencing datasets.

    o The main function of the package (processPipeline) provides an
    automated pipeline with a bunch of options designed to transform
    reads to a comprehensive 'score per genomic coordinates' format 
    (implemented as WIG files fixed or variable step). This process
    involves the automatic estimation of sequenced fragments length.

    o The pipeline give statistics about users datasets which help to
    have an idea about data quality and take appropriate decisions for
    data processing steps.

    o The pipeline provides specific options and behaviour adapted to
    paired-end aligned reads and gives several innovative options for
    piling the read scores (midpoint...).

    o Included in the package are some additional functions designed 
    to help the user dealing with WIG fixed step format (merging
    files, rescaling, subtracting...)  

    o Please see the manual pages and associated vignette for more
    detailed information about how to use this resource.