# REMP 0.99.0 *初始提交Bioconductor。# REMP 0.99.14 *修正基于初始提交的评论。# REMP 0.99.16 *包Bioconductor所接受。# REMP 0.99.20 *添加修剪(REMProduct)功能调整的基础上预测了论文认定质量分数对随机森林模型(只)。# REMP 0.99.21 *改进的健壮性函数GRannot()当指标列“指数”没有提供;*固定不准确的重新统计数据计算后修剪()函数。# REMP 0.99.22 *启用并行计算功能decodeAnnot (REMProduct)。# REMP 0.99.24 *片段更新*固定bug Mac OS和Linux系统。# REMP 0.99.25 *固定超时问题中遇到的构建系统。# REMP 1.0.0 * Bioconductor最初版本。 # 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. # REMP 1.10.1 * REMP package now supports Long Terminal Repeat (LTR), including Endogenous Retroviruses (ERV) * Fixed bug in function 'grooMethy'. # REMP 1.20.1 * AnnotationHub database for RepeatMasker is updated (both hg19 and hg38). * Long Terminal Repeat (LTR) is renamed to Endogenous Retrovirus (ERV). * The UCSC annotation database source is disabled in function fetchRMSK. AnnotationHub provides more accurate class and family definition.