CHANGES IN VERSION 1.14.0 ------------------------- o Bioconductor 3.17 release CHANGES IN VERSION 1.12.0 ------------------------- o Bioconductor 3.16 release CHANGES IN VERSION 1.10.0 ------------------------- o Bioconductor 3.15 release CHANGES IN VERSION 1.8.1 ------------------------- o added grid to Imports o fixed citation o updated DOI CHANGES IN VERSION 1.8.0 ------------------------- o Bioconductor 3.14 release CHANGES IN VERSION 1.6.0 ------------------------- o Bioconductor 3.13 release CHANGES IN VERSION 1.4.0 ------------------------- o Bioconductor 3.12 release CHANGES IN VERSION 1.2.2 ------------------------- o skipped Python-dependent tests on i386 systems (64-bit version of Python is required) CHANGES IN VERSION 1.2.0 ------------------------- o added blue background to IDR distribution histograms o updated roxygen2 version to 7.1.0 o added unit tests CHANGES IN VERSION 1.0.4 ------------------------- o changed max_gap default value from 0 to -1 to conform with convention o updated reference to IDR2D publication CHANGES IN VERSION 1.0.3 ------------------------- o added option to disable jitter o added min_value and max_value parameters to estimate_idr2d_hic o fix block size display for draw_hic_contact_map CHANGES IN VERSION 1.0.2 ------------------------- o added parser for HiC-Pro contact maps (.matrix and .bed files) o added function to visualize contact maps, showing only reproducible blocks CHANGES IN VERSION 1.0.1 ------------------------- o fixed alpha level in rank and value scatterplots o bold font face for axis and legend titles CHANGES IN VERSION 1.0.0 ------------------------- o added HiC code example o added summary statistics to IDR1D, IDR2D, IDR2D HiC results o added summary calls to vignettes o added alpha parameter to control transparency CHANGES IN VERSION 0.99.7 ------------------------- o refactored HiC code CHANGES IN VERSION 0.99.6 ------------------------- o added optional log scale axes to plotting functions o added error handling o adjusted log messages o added log_idr argument o added min value / max value filtering o mentioned typical HiC resolutions CHANGES IN VERSION 0.99.5 ------------------------- o fixed minor code formatting and function documentation issues o changed function names from lower camel case to snake case o updated reference in vignettes o replaced dots in variable names with underscores o added HiC functionality CHANGES IN VERSION 0.99.4 ------------------------- o fixed issue with non-standard column names o added examples to function documentation CHANGES IN VERSION 0.99.3 ------------------------- o added max.points.shown parameter CHANGES IN VERSION 0.99.2 ------------------------- o added consistent ticks and limits to IDR plot functions o updated function documentation CHANGES IN VERSION 0.99.1 ------------------------- o added reference to Li et al. paper o added diagnostics plots o changed rank order o added IDR1D functionality o fixed local / global IDR issue CHANGES IN VERSION 0.99.0 ------------------------- o initial release