New vignette for Bioconductor resubmission

This release contains an improved version of the vignette and a minor bug fix.

Bioconductor pre-release

The version of CopywriteR (previously known as ENCODER) is fully Bioconductor-compatible and has major advantages to the previous release. The required helper files can now be downloaded as an annotation package (CopyhelpeR) from this link. Other improvements include:

• Removing the requirement for non-R tools (MACS1.4, bedtools, samtools)
• Implementing BiocParallel for parallel computing to allow more flexibility
• Helper files can now be downloaded as an anntation package
• Replacing .bed files for GRanges objects
• Making output file readable in IGV
• Moving to 1-based notation for compatibility with Bioconductor
• Improving log-file
• Improving user-friendliness
• Providing the option to keep intermediary files; remove these by default
• Improving file integrity and folder permission checks
• Implementing DNAcopy for segmentation rather than CGHcall
• Improving the plotting function
• Changing input structure to allow more flexibility

Support for alternative chromosome names

This new release implements support for alternative chromosome naming (i.e., 'chr1' instead of '1'). The only requirement is that the chromosome notation in the helper files and in the .bam files match. This version of CopywriteR checks whether all .bam files have the same chromosome naming, and that the helper files match this notation; CopywriteR provides error messages if this is not the case.

Now compatible with mm9, mm10 (mouse genomes) and hg19 (human genome)

In this release we have included compatibility with mm9 and mm10 mouse genomes. The mapability, GC-content and blacklist files can be created using preENCODER and the mm9_1kb or mm10_1kb folder as input.

Many bug fixes

This release contains many bug fixes, including the fact that now single-end sequencing data can be used by ENCODER too. Also, the captureRegionsBedFile is now optional, and the code has been optimized. Parallellization is now al using snowfall and the doParallel package has been removed from the code.

Pre-compiled ENCODER R-package

This is the first release version of ENCODER. It includes the complete pre-compiled R-package and the annotation files for human hg19.
Annotation files for mm10 are not included yet but will be in the next release.