Changes in version 2026-06-09 *Removed the HiCseg dependency, which was archived from CRAN. getAsymmetricBlockIndices() now defaults to algorithm="jointSeg"; HiCseg is still used where it is installed. Changes in version 2022-08-12 *Updated NCI Policies on Server UI Changes in version 2021-06-17 *Minor change to ensure compatibility with multiple datasets. Changes in version 2021-05-19 *Require R-4.1.0 in order to make the package CRAN compliant (fixes a single rtracklayer check server install issue) Changes in version 2021-05-14 *Following CRAN guidance, removed a command to close all connections after opening a file. Changes in version 2021-01-07 *Bug fixes related to the suggested plotly dependency. Changes in version 2021-01-05 *Moved the plotly package to suggests because it has been temporarily orphaned. Changes in version 2021-01-04 *Made package check successfully without suggested dependencies. Changes in version 2020-12-15 *Made conditional BSgenome.Hsapiens.UCSC.hg19 to improve OSX installation. Changes in version 2020-12-14 *Made conditional InteractionSet to make OSX installation more seamless. Changes in version 2020-11-28 *We have now added smoothie::kernel2d smooth as an alternative smoother to spatialfil (now disabled) and now our package should once again be CRAN ready. Changes in version 2020-11-27 *With spatialfil removed from CRAN, we have disabled the spatialfil requirement to run the additional examples. *This algorithm is neat and we'll look at other ways to calculate interaction probability, but for the moment, we'll just disable things to keep the package on CRAN. Changes in version 2020-8-14 *Fixed the gene search in the shiny application *Added gene listing for row and column genes to the left of the plot. **These gene data table outputs are searchable and the size is adjustable. *Disabled automatic switching to the sample data tab on click so that users can properly use the new gene column feature. *CRAN fixes to keep the package publicly available Changes in version 2020-7-2 *Reduced imports to 20 and moved the remainder of packages into suggests. *Fixed whole genome map. *Optimized load time to plot a whole genome map (should be roughly a 50% reduction, according to profvis). Changes in version 2019-12-7 *Removed Biostrings dependency to clear NOTE (although packages that CNVScope depends on require it). The prior Biostrings issue has been fixed. Changes in version 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. Changes in version 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. *Removed blockseg as a strong dependency, per CRAN. Changes in version 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. Changes in version 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 2.7.2.5. *passes CRAN checks again with flying colors (no notes, warnings, or errors). Changes in version 2019-09-21 *Added P-value filter *Added correlatoin options *Added additional app visualization options. *Added material on how to make higher resolution maps. Changes in version 2019-07-19 *Minor changes to package dependency CNVScopePublicData. Changes in version 2019-07-18 *Another minor cran fix to CNVScopeserver. *Small changes to CNVScopeserver to fix a CRAN check. Changes in version 2019-07-17 *Small changes to dependencies (including pwr package) and vignettes. Changes in version 2019-07-16 *Minor fix to freadGDCfile documentation Changes in version 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. Changes in version 2019-07-09 Changes: - Fixed vignettes not properly linking to the package. CNVScope v2.4.4 (Release date: 2019-07-09) ============== Changes: - Added a power analysis vignette - Fixed issues with formSampleMatrixFromRawGDCData ** These issues arose from changing types with underlying Bioconductor dependencies from character to factor Rle. - Updated the build for R-base v3.6.1 *prior to this, this package now works with CNVScopePublicData, a large package containing *all that is requisite to run the server locally.