# REMP 0.99.0 * Initial submission to Bioconductor. # REMP 0.99.14 * Revisions based on the comments to the initial submission. # REMP 0.99.16 * Package accepted by Bioconductor. # REMP 0.99.20 * Added trim(REMProduct) functionality to trim predicted CpGs based on quality score (only for Random Forest model). # REMP 0.99.21 * Improved the robustness of function GRannot() when indicator column "Index" is not provided; * Fixed the inaccurate RE statistics calculation after function trim() is applied. # REMP 0.99.22 * Enabled parallel computing in function decodeAnnot(REMProduct). # REMP 0.99.24 * Vignettes updated * Fixed bugs for Mac OS and Linux system. # REMP 0.99.25 * Fixed timeout issue encountered in the build system. # REMP 1.0.0 * Initial release on Bioconductor. # REMP 1.0.1 * In groomethy, changed the default KNN imputation direction from "by-column" to "by-row" to avoid out-of-range imputation results. # REMP 1.0.4 * Use package 'ranger' to boost computation speed for Random Forest. # REMP 1.0.7 * Allow random seed for reproducible results using Random Forest; * Use package 'ranger' to simplfy the code and boost computation speed for Quantile Regression Forest. # REMP 1.2.1 * Added "rempAggregate" method to "REMProduct" class to enable aggregation algorithm; * Function name changed: annotation --> rempAnnot, trim --> rempTrim, imp --> rempImp; * Fixed a bug when using "naive" method. # REMP 1.2.3 * Allows parallel computing in "rempAggregate" method; * Added "rempCombine" method to combine two "REMProduct" objects by column. # REMP 1.2.5 * Added "remprofile" method to get the methylation data profiled in RE; * Minor bug fixes and improvements. # REMP 1.4.0 * Version number update (same as REMP 1.2.5). R-3.5.0. Bioconductor 3.7. # REMP 1.4.1 * Fixed bug in grooMethy; * Added parameters to control the behaviors of imputation in "remprofile". # REMP 1.8.1 * REMP package now supports methylation sequencing data as input; * "remp" function now supports Extreme Gradient Boosting model; * Added new function 'rempTemplate' to facilitate model parameter tunning; * Fixed bug in identifying numbers of back-end workers; * Fixed bug in predictor importance matrix; * Improved robustness. # REMP 1.8.2 * REMP package now supports genome build hg38; * Alternative versions of annotation databases can now be accessed from UCSC websites.