# 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. 

# 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.
