CHANGES IN VERSION 1.3
----------------------

OVERVIEW

    o systemPipeR is an R/Bioconductor package for building and running automated
      analysis workflows for a wide range of next generation sequence (NGS)
      applications. Important features include a uniform workflow interface
      across different NGS applications, automated report generation, and support
      for running both R and command-line software, such as NGS aligners or
      peak/variant callers, on local computers or compute clusters. Efficient
      handling of complex sample sets and experimental designs is facilitated by
      a consistently implemented sample annotation infrastructure.

    o The most important enhancements in the upcoming release of the package are 
      outlined below.  
    
NGS WORKFLOWS

    o Added new end-to-end workflows for 3 additional NGS application areas: 
        - Ribo-Seq and polyRibo-Seq 
        - ChIP-Seq
        - VAR-Seq
      The previous version of systemPipeR included only a complete workflow for
      RNA-Seq.

    o Added the data package 'systemPipeRdata' to generate systemPipeR workflow
      environments with a single command (genWorkenvir) containing all parameter
      files and sample data required to quickly test and run workflows. This
      change will also allow evaluation of much more code examples in the
      vignettes during the package build/test process than this was possible in
      the past. 

    o About 20 new functions have been added to the package. Some examples are:
        - Read pre-processor function with support for SE and PE reads
        - Parallelization option of detailed FASTQ quality reports
        - Read distribution plots across all features available in a 
          genome annotation (see ?featuretypeCounts) 
        - Visualization of coverage trends along transcripts summarized 
          for any number of transcripts (see ?featureCoverage)
        - Functionalities to predict uORFs/sORFs and to use them for expression profiling
        - Differential expression/binding analysis includes now DESeq2 as
          well as edgeR

    o Added param templates for additional command-line software including, but 
      not limited to: BWA-MEM, GATK, BCFtools, MACS2

    o Adoption of R Markdown for main vignette. Future plans are to provide for
      all workflows the report templates in both formats: Latex/PDF and
      R_Markdown/HTML.

WORFLOW FRAMEWORK

    o Simplified design of complex analysis workflows. Workflows can now include
      any number or combination of R and/or command-line steps

    o Improvements to workflow automation and parallelization on single
      machines and computer clusters. This also includes now many additional
      parallelization examples in the workflow vignettes.


