RnBeads 1.99.0
=============
 
 * RnBeadsDJ: updated documentation and tooltips
 * deactivated intersample plots (exploratory module) as default option for BS-seq data
 * Roxygen documentation updates
 * Extended methods descriptions in reports (imputation, filtering, differential, ...)
 * Miscellaneous bugfixes and performance improvements in RnBeadsDJ, imputation, ...

RnBeads 1.13.3
=============
 
 * added CNV estimation using the GLAD package to QC module
 * some bugfixes
 * changed 'gender' to 'sex', affected functions and options are 'rnb.execute.gender.prediction' and 'import.gender.prediction'

RnBeads 1.13.2
=============
 
 * added qvalue to suggested packages

RnBeads 1.13.1
=============
 
 * Updated LOLA DB download links

RnBeads 1.11.9
=============
 
 * Bugfixes and improvements in gender prediction, GEO import, differential variability, installation and others

RnBeads 1.11.8
=============
 
 * Fixes for bioconductor warnings (combine, etc.)
 * docoupled missing value imputation from differential methylation

RnBeads 1.11.7
=============
 
 * enhanced cross-platform combination methods
 * improved installation routines
 * enhanced plots in exploratory analysis module
 * better LOLA annotation
 * improved performance of missing value imputation
 * documentation updates
 * several minor bugfixes

RnBeads 1.11.6
=============
 
 * Improved combining methods for RnBSet objects of different data types
 * Interpretation of sample mean methylation levels and other statistics
 * Improved plots in exploratory analysis module
 * Improved missing value imputation
 * Several minor bugfixes

RnBeads 1.11.5
=============
 
 * bugfixes (loading, imputation)

RnBeads 1.11.4
=============
 
 * Introducing RnBeadsDJ, a shiny-based interface for running RnBeads analyses and modules (run with rnb.run.dj())
 * Added implementation of the LUMP algorithm for immune cell content estimation
 * The default normalization method was changed to "wm.dasen"
 * Background normalization is now disabled per default.
 * Option backwards compatibility
 * bugfixes (LOLA dependencies, 1-sample differential variability, QC visualization, ...)

RnBeads 1.11.2
=============

 * Fixed a bug concerning failed trackhub exports on Windows

RnBeads 1.9.4
=============

 * You can now retrieve custom region sets from the RnBeads resource using the rnb.load.annotation.from.db function
 * improved import from GEO
 * bigff disk dump is now the default option for dealing with disk-based big matrices
 * Several bugfixes and performance improvements in Greedycut, normalization, Bisulfite data loading and others
 * Added differential variability analysis in addition to differential methylation

RnBeads 1.9.3
=============

 * LOLA support for differentially methylated regions
 * various LOLA utitility functions
 * What used to be the "differential.enrichment" option is now called "differential.enrichment.go" to reflect the distinction between GO and LOLA enrichment analyses
 * Missing methylation data can now be imputed (using mean, random or nearest-neighbor imputation)
 * Gender prediction now supports sequencing and EPIC data
 * Added a function for combining two array-based datasets from (potentially) different platforms.
 * Several bugfixes and performance improvements

RnBeads 1.7.5
=============

 * Several minor bugfixes and performance improvements
 * added a vignette section on working with RnBSet objects 

RnBeads 1.7.4
=============

 * Several minor bugfixes and performance improvements
 * Vignette installation instructions updated
 * Reduce warnings in R CMD check

RnBeads 1.7.3
=============

 * Age predictor (MethylAger) updates and documentation
 * Support for external tools bedToBigBed and bedGraphToBigWig
 * Minor bugfixes

RnBeads 1.7.2
=============

 * Added genetic purity estimation based on SNP probes (option qc.snp.purity, microarrays only)

RnBeads 1.7.1
=============

 * Added support for the ENmix.oob background subtraction method
 * Several improvements in age prediction module
 * Added conversion from minfi raw dataset to RnBeadRawSet
 * Several minor bug fixes

RnBeads 1.5.1
=============

 * Reference-based cell type composition estimation now uses the 50,000 most variable sites by default.
 * Minor bug fixes

RnBeads 1.3.8
=============

 * Added age prediction from 450K and bisulfite data to inference module

RnBeads 1.3.7
=============

 * Subsampling for reporting and plotting methylation values distributions in filtering
   report to reduce memory footprint.

RnBeads 1.3.6
=============

 * Support for Illumina EPIC array and related bugfixes
 * Added a section on whitelist and blacklist in the Preprocessing module

RnBeads 1.3.5
=============

 * Fixes with ggplot in 450K array QC plotting
 * Added an option 'differential.report.sites' to decrease runtime by skipping the differential site methylation section in the report

RnBeads 1.3.4
=============

 * Added support for Illumina EPIC array

RnBeads 1.3.3
=============

 * Added 'smooth.profile' parameter to rnb.plot.locus.profile function

RnBeads 1.3.2
=============

 * Performance and memory improvements during loading, qc and preprocessing of large bisulfite-derived RnBSets
 * Added optional arguments to meth() and covg() allowing for partial retrieval of methylation and coverage information from RnBSets. Particularly makes sense for large, disk-based datasets.
 * Added option "disk.dump.bigff.finalizer" for setting the finalizer for temporary BigFfMat objects

RnBeads 1.3.1
=============

 * Added "remove.regions" function for RnBSet class
 * summarize.regions now summarizes for each sample individually in order to reduce memory consumption for large WGBS datasets
 * import.skip.object.check option for keeping the memory profile low while loading huge datasets
 * NA sites (filtering.missing.value.quantile) are now removed even if they were previously masked (filtering.low.coverage.masking)
 * Added "nsites" method for quickly extracting the number of sites for large RnBSet objects without having to retrieve the full methylation matrix
 * Added "hasCovg" method for quickly determining whether coverage information is present in large RnBSet objects without having to retrieve the full coverage matrix

RnBeads 1.1.9
=============

 * Filtering report fix when no normalization is conducted
 * Bugfixes for combine(RnBSet, RnBSet) and BigFf matrices

RnBeads 1.1.8
=============

 * Corrected coverage statistics in sample summary table: Sites with NA methylation values are no longer considered in the coverage statistics (makes a difference if some coverage threshold is applied)
 * Improved method for gender prediction. Predicted genders are also included in the exported annotation table

RnBeads 1.1.7
=============

 * Improvements to mergeSamples function for RnBiseqSets
 * Some more memory clean-up

RnBeads 1.1.6
=============

 * Differential methylation based on region level only is now supported
 * Minor updates to the differential methylation report generation
 * Performance improvements and minor bugfixes for using disk.dump.bigff
 * Performance improvements (more memory clean-up)


RnBeads 1.1.5
=============

 * New option: disk.dump.bigff for using a wrapper class of the ff package to avoid their INT_MAX issue

RnBeads 1.1.4
=============

 * Fixes in parallel environment setup from bioconcuctor

RnBeads 1.1.3
=============

 * Some fixes in data loading
 * Fixes in parallel environment setup

RnBeads 1.1.2
=============

 * New annotation package format
 * Support for filtering out cross-reactive probes in Infinium 450k dataset
 * Improved logging on a Mac

RnBeads 1.0.0
=============

 * Bioconductor release

RnBeads 0.99.23
===============

 * Incorporated some bioconductor check related improvements

RnBeads 0.99.22
===============

 * Incorporated bioconductor requirements for parallel processing. "parallel.disable" is now "parallel.teardown"

RnBeads 0.99.20
===============

 * RnBeads no longer suggests IlluminaHumanMethylation450k.db.

RnBeads 0.99.19
===============

 * Fixed a bug in the computation of surrogate variables (SVA) that did not take into account other adjustment variables in the model (compared to the null model)
 * Updated locus profiles to work with the latest version of Gviz
 * Differential methylation reports now contain information on group sizes
 * Included plots of number of sites vs coverage percentiles for each sample in the dataset (rnb.plot.num.sites.covg)
 * Bisulfite-seq QC reports now contain an additional section with summary statistics and plots when the coverage histogram plots are enabled

RnBeads 0.99.18
===============

 * Implementation of class constructors (the S4 constructors are not available anymore)
 * Analyses can now be started from an RnBSet which is stored on the hard drive (using save.rnb.set) via the rnb.set.dir data type
 * New IDAT loading routine, based on the illuminaio package
 * Multiple fixes in wrappers for wateRmelon normalization methods
 * Fixed the RefFreeEWAS wrapper
 * Updated the Houseman, 2012 reference-based method implementation
 * RnBSets now know the version with which they were created
 * Various other bugfixes and improvements to reports and documentation

RnBeads 0.99.17
===============

 * Consistency issues with Bioconductor 3.0 fixed
 * Fixed a bug relating to no coverage masking being conducted for sequencing data
 * Various other bugfixes

RnBeads 0.99.16
===============

 * Enhanced XML-based analysis though the tag preanalysis.script
 * Optimized loading of the sequencing data sets
 * Enhanced region profiles plots. Added region site distribution plots
 * Locus profiles can now be generated in the exploratory report for regions specified in custom bed files and for genes listed as gene symbols
 * Improved cell type heterogeneity inference (no cell types excluded anymore)
 * Added more support for paired differential methylation with limma
 * Some functions were renamed: merge.samples->mergeSamples, add.pheno->addPheno, add.region.subsegments->addRegionSubsegments, and all functions operating on Report
 * Added helper classes for submitting RnBeads to a scientific compute cluster. Current implementation includes Sun Grid Engine
 * The default pipeline now uses ff functionality and saves intermediate objects into the report directory
 * Minor bugfixes

RnBeads 0.99.15
===============

 * Restructuring of the pipeline modules:
 ** the loading module has been renamed to import
 ** the prefiltering,normalization and postfiltering modules have been summarized in a new module: preprocessing
 ** the batch and profiles modules have been summarized in a new module for exploratory analysis
 ** the export module has been renamed to tracks and tables
 ** corresponding option names have been changed
 ** see the overview figure on the website or the vignette for a quick overview on the new module structure
 * Multiple RnBSets can now be concatenated with the add() function
 * Multiple samples in an RnBSet can be merged using the merge.samples() function
 * Gender prediction can be performed on Infinium 450k datasets
 * Minor updates on covariate adjustment
 * Updates on tissue heterogeneity estimation
 * Calling differentially methylated sites with RefFreeEWAS now supports paired design
 * Multiple minor bugfixes and performance improvements
 * Vignette and documentation updates

RnBeads 0.99.13
===============

 * Added new module on annotation inference
 * Added correction for cell type heterogeneity
 * Added SVA functionality
 * Minor bugfixes
 * Updates to the vignette and other documentation

RnBeads 0.99.12
===============

 * Support Bismark coverage file loading
 * Enhanced documentation and logging of loading steps
 * Minor bugfixes
 * Updates to the vignette and other documentation

 RnBeads 0.99.11
===============

 * Accommodate data packages for individual genomes
 * Performance: disk space usage when using disk dumping, options for subsetting sites when computing distance matrices for clustering, PCA and MDS
 * Region subsegmentation
 * The default method for differential methylation p-values is limma

RnBeads 0.99.10
===============

 * Performance improvements
 * Option to keep big matrices on the hard drive rather than main memory
 * Restructuring of the filtering modules. Parts of the filtering steps are executed before normalization others afterwards
 * Improvements in normalization: more methods supported
 * Cosmetic changes to some of the plots

RnBeads 0.99.9
==============

 * Bugfixes in paired analysis
 * Usability of bisulfite sequencing

RnBeads 0.99.8
==============

 * New normalization methods integrated
 * Improved arguments to rnb.run.analysis
 * Improved parsing of the sample annotation table
 * Paired analysis (testing stage)
 * Webservice installed
 * Multiple bugfixes

RnBeads 0.99.7
==============

 * Support for background subtraction and BMIQ normalization of Infinium 450k data
 * Support for differential methylation analysis on all pairs of sample groups

RnBeads 0.99.6
==============

 * Locus Profiles
 * Support for parallel computing

RnBeads 0.99.0
==============

 * Many additional features including bisulfite sequencing mode, the mouse genome, data export, ...

RnBeads 0.5.0
=============

 * Initial release of RnBeads containing six modules - loading and normalization, quality control, filtering, batch effects, methylation profiles and differential methylation.
