CNVScope v2.9.4 (Release Date 2019-12-7)

*Removed Biostrings dependency to clear NOTE (although packages that CNVScope depends on require it). The prior Biostrings issue has been fixed.

CNVScope v2.9.2 (Release Date 2019-12-5)

Added an explicit dependency, Biostrings to keep CRAN check errors on debian from occurring. Made a small fix to rebinGenomicInteractions, fixing a check at the end to handle a vector input **This will make the package compatible with R 4.0.

CNVScope v2.8.2 (Release Date 2019-10-23)

*Removed all blockseg references in code. It was a nice feature to have a third algorithm, but blockseg will not be on CRAN shortly.

CNVScope v2.8.1 (Release Date 2019-10-23)

*Removed blockseg as a strong dependency, per CRAN.

CNVScope v2.7.7 (Release Date 2019-10-18)

Updated documentation (some new images have been added to show the effect of bin sizes and resolution). Fixed a broken URL that was causing a CRAN note.

CNVScope v2.7.5 (Release Date 2019-10-12)

Updated documentation for finely binned matrices (see the input matrix vignette). Several sizes of NBL whole genome matrices are available within the package (1e5,2.5e5,1e6,1e7,1e8). These are for package use only. The HD matrices are not speed-optimal for app use. Functionality of basic package functions remains the same as *passes CRAN checks again with flying colors (no notes, warnings, or errors).

CNVScope v2.7.2.5 (Release Date 2019-09-21)

Added P-value filter Added correlatoin options Added additional app visualization options. Added material on how to make higher resolution maps.

CNVScope v2.5.4 (Release date: 2019-07-19)

*Minor changes to package dependency CNVScopePublicData.

CNVScope v2.5.2 (Release date: 2019-07-18)

*Another minor cran fix to CNVScopeserver.

CNVScope v2.5.1 (Release date: 2019-07-18)

*Small changes to CNVScopeserver to fix a CRAN check.

CNVScope v2.5.0 (Release date: 2019-07-18)

Small changes in 2.4.9 to the README, for publicity. Major changes to many functions to pass CRAN checks (global variable issues). CNVScope v2.4.8 (Release date: 2019-07-17) ============== *Small changes to dependencies (including pwr package) and vignettes.

CNVScope v2.4.7 (Release date: 2019-07-16)

*Minor fix to freadGDCfile documentation

CNVScope v2.4.6 (Release date: 2019-07-15)

More information about BLCA, SKCM, and AML in additional examples vignette Their processed files have been placed within the package These are available only on the github site as the CRAN size limitations forbid it. Added the ability to specify chrM and chrY in formSampleMatrixFromRawGDCData function.

CNVScope v2.4.4 (Release date: 2019-07-09)

Changes: * Fixed vignettes not properly linking to the package. CNVScope v2.4.4 (Release date: 2019-07-09) ==============