Changes in version 2.27.3 o Implemented XenoMix for estimating mouse content from EPIC array data in PDX models Changes in version 2.27.1 o Fixed issue with nv probes. Now they are filtered during the preprocessing. Changes in version 2.19.0 o Fixed issue with logical having a length greater than 1 Changes in version 2.17.1 o Temporarily removed the GLAD dependency and CNV functionality Changes in version 2.17.0 o Fixed bug in differential variability analysis Changes in version 2.15.1 o Added custom reimplementations of dye-bias and background correction methods from SeSaMe Changes in version 2.13.2 o Removed support for RefFreeEWAS, since the package is not supported anymore Changes in version 2.13.0 o Compatibility fixes with SeSaMe by zwdzwd o Minor bugfixes Changes in version 2.11.0 o Bugfixes in MMBC support Changes in version 2.9.4 o Added initial version of the Mouse Methylation Bead Chip support o Native implementations of basic dye-bias and background correction methods (methylumi dependency removed) Changes in version 2.9.3 o Changed some of the default options values o Some bugfixes Changes in version 2.9.2 o Implemented function rnb.execute.pOOBAH. Thanks to Nathan Steenbuck. o Update of contact information in DESCRIPTION Changes in version 2.9.1 o Improved function intensities.by.color. Thanks to Nathan Steenbuck. Changes in version 2.7.1 o Added conversion from RnBeadRawSet to RGChannelSet Changes in version 2.3.3 o Fixed non ASCII column names in age prediction and immune estimation Changes in version 2.3.2 o Added stratification plots for inferred covariates in different sample groups Changes in version 2.1.3 o Implemented methylation based segmentation by the MethylSeekR approach. Thanks to Abdulrahman Salhab for providing code for the integration. o Wrapper for load.rnb.set Changes in version 2.1.2 o Fix in as.RnBeadRawSet o Added new paper to CITATION Changes in version 2.1.1 o Added support for SLURM compute cluster architecture Changes in version 1.99.0 o RnBeadsDJ: updated documentation and tooltips o deactivated intersample plots (exploratory module) as default option for BS-seq data o Roxygen documentation updates o Extended methods descriptions in reports (imputation, filtering, differential, ...) o Miscellaneous bugfixes and performance improvements in RnBeadsDJ, imputation, ... Changes in version 1.13.3 o added CNV estimation using the GLAD package to QC module o some bugfixes o changed 'gender' to 'sex', affected functions and options are 'rnb.execute.gender.prediction' and 'import.gender.prediction' Changes in version 1.13.2 o added qvalue to suggested packages Changes in version 1.13.1 o Updated LOLA DB download links Changes in version 1.11.9 o Bugfixes and improvements in gender prediction, GEO import, differential variability, installation and others Changes in version 1.11.8 o Fixes for bioconductor warnings (combine, etc.) o docoupled missing value imputation from differential methylation Changes in version 1.11.7 o enhanced cross-platform combination methods o improved installation routines o enhanced plots in exploratory analysis module o better LOLA annotation o improved performance of missing value imputation o documentation updates o several minor bugfixes Changes in version 1.11.6 o Improved combining methods for RnBSet objects of different data types o Interpretation of sample mean methylation levels and other statistics o Improved plots in exploratory analysis module o Improved missing value imputation o Several minor bugfixes Changes in version 1.11.5 o bugfixes (loading, imputation) Changes in version 1.11.4 o Introducing RnBeadsDJ, a shiny-based interface for running RnBeads analyses and modules (run with rnb.run.dj()) o Added implementation of the LUMP algorithm for immune cell content estimation o The default normalization method was changed to "wm.dasen" o Background normalization is now disabled per default. o Option backwards compatibility o bugfixes (LOLA dependencies, 1-sample differential variability, QC visualization, ...) Changes in version 1.11.2 o Fixed a bug concerning failed trackhub exports on Windows Changes in version 1.9.4 o You can now retrieve custom region sets from the RnBeads resource using the rnb.load.annotation.from.db function o improved import from GEO o bigff disk dump is now the default option for dealing with disk-based big matrices o Several bugfixes and performance improvements in Greedycut, normalization, Bisulfite data loading and others o Added differential variability analysis in addition to differential methylation Changes in version 1.9.3 o LOLA support for differentially methylated regions o various LOLA utitility functions o What used to be the "differential.enrichment" option is now called "differential.enrichment.go" to reflect the distinction between GO and LOLA enrichment analyses o Missing methylation data can now be imputed (using mean, random or nearest-neighbor imputation) o Gender prediction now supports sequencing and EPIC data o Added a function for combining two array-based datasets from (potentially) different platforms. o Several bugfixes and performance improvements Changes in version 1.7.5 o Several minor bugfixes and performance improvements o added a vignette section on working with RnBSet objects Changes in version 1.7.4 o Several minor bugfixes and performance improvements o Vignette installation instructions updated o Reduce warnings in R CMD check Changes in version 1.7.3 o Age predictor (MethylAger) updates and documentation o Support for external tools bedToBigBed and bedGraphToBigWig o Minor bugfixes Changes in version 1.7.2 o Added genetic purity estimation based on SNP probes (option qc.snp.purity, microarrays only) Changes in version 1.7.1 o Added support for the ENmix.oob background subtraction method o Several improvements in age prediction module o Added conversion from minfi raw dataset to RnBeadRawSet o Several minor bug fixes Changes in version 1.5.1 o Reference-based cell type composition estimation now uses the 50,000 most variable sites by default. o Minor bug fixes Changes in version 1.3.8 o Added age prediction from 450K and bisulfite data to inference module Changes in version 1.3.7 o Subsampling for reporting and plotting methylation values distributions in filtering report to reduce memory footprint. Changes in version 1.3.6 o Support for Illumina EPIC array and related bugfixes o Added a section on whitelist and blacklist in the Preprocessing module Changes in version 1.3.5 o Fixes with ggplot in 450K array QC plotting o Added an option 'differential.report.sites' to decrease runtime by skipping the differential site methylation section in the report Changes in version 1.3.4 o Added support for Illumina EPIC array Changes in version 1.3.3 o Added 'smooth.profile' parameter to rnb.plot.locus.profile function Changes in version 1.3.2 o Performance and memory improvements during loading, qc and preprocessing of large bisulfite-derived RnBSets o 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. o Added option "disk.dump.bigff.finalizer" for setting the finalizer for temporary BigFfMat objects Changes in version 1.3.1 o Added "remove.regions" function for RnBSet class o summarize.regions now summarizes for each sample individually in order to reduce memory consumption for large WGBS datasets o import.skip.object.check option for keeping the memory profile low while loading huge datasets o NA sites (filtering.missing.value.quantile) are now removed even if they were previously masked (filtering.low.coverage.masking) o Added "nsites" method for quickly extracting the number of sites for large RnBSet objects without having to retrieve the full methylation matrix o Added "hasCovg" method for quickly determining whether coverage information is present in large RnBSet objects without having to retrieve the full coverage matrix Changes in version 1.1.9 o Filtering report fix when no normalization is conducted o Bugfixes for combine(RnBSet, RnBSet) and BigFf matrices Changes in version 1.1.8 o 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) o Improved method for gender prediction. Predicted genders are also included in the exported annotation table Changes in version 1.1.7 o Improvements to mergeSamples function for RnBiseqSets o Some more memory clean-up Changes in version 1.1.6 o Differential methylation based on region level only is now supported o Minor updates to the differential methylation report generation o Performance improvements and minor bugfixes for using disk.dump.bigff o Performance improvements (more memory clean-up) Changes in version 1.1.5 o New option: disk.dump.bigff for using a wrapper class of the ff package to avoid their INT_MAX issue Changes in version 1.1.4 o Fixes in parallel environment setup from bioconcuctor Changes in version 1.1.3 o Some fixes in data loading o Fixes in parallel environment setup Changes in version 1.1.2 o New annotation package format o Support for filtering out cross-reactive probes in Infinium 450k dataset o Improved logging on a Mac Changes in version 1.0.0 o Bioconductor release Changes in version 0.99.23 o Incorporated some bioconductor check related improvements Changes in version 0.99.22 o Incorporated bioconductor requirements for parallel processing. "parallel.disable" is now "parallel.teardown" Changes in version 0.99.20 o RnBeads no longer suggests IlluminaHumanMethylation450k.db. Changes in version 0.99.19 o 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) o Updated locus profiles to work with the latest version of Gviz o Differential methylation reports now contain information on group sizes o Included plots of number of sites vs coverage percentiles for each sample in the dataset (rnb.plot.num.sites.covg) o Bisulfite-seq QC reports now contain an additional section with summary statistics and plots when the coverage histogram plots are enabled Changes in version 0.99.18 o Implementation of class constructors (the S4 constructors are not available anymore) o 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 o New IDAT loading routine, based on the illuminaio package o Multiple fixes in wrappers for wateRmelon normalization methods o Fixed the RefFreeEWAS wrapper o Updated the Houseman, 2012 reference-based method implementation o RnBSets now know the version with which they were created o Various other bugfixes and improvements to reports and documentation Changes in version 0.99.17 o Consistency issues with Bioconductor 3.0 fixed o Fixed a bug relating to no coverage masking being conducted for sequencing data o Various other bugfixes Changes in version 0.99.16 o Enhanced XML-based analysis though the tag preanalysis.script o Optimized loading of the sequencing data sets o Enhanced region profiles plots. Added region site distribution plots o Locus profiles can now be generated in the exploratory report for regions specified in custom bed files and for genes listed as gene symbols o Improved cell type heterogeneity inference (no cell types excluded anymore) o Added more support for paired differential methylation with limma o Some functions were renamed: merge.samples->mergeSamples, add.pheno->addPheno, add.region.subsegments->addRegionSubsegments, and all functions operating on Report o Added helper classes for submitting RnBeads to a scientific compute cluster. Current implementation includes Sun Grid Engine o The default pipeline now uses ff functionality and saves intermediate objects into the report directory o Minor bugfixes Changes in version 0.99.15 o 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 o Multiple RnBSets can now be concatenated with the add() function o Multiple samples in an RnBSet can be merged using the merge.samples() function o Gender prediction can be performed on Infinium 450k datasets o Minor updates on covariate adjustment o Updates on tissue heterogeneity estimation o Calling differentially methylated sites with RefFreeEWAS now supports paired design o Multiple minor bugfixes and performance improvements o Vignette and documentation updates Changes in version 0.99.13 o Added new module on annotation inference o Added correction for cell type heterogeneity o Added SVA functionality o Minor bugfixes o Updates to the vignette and other documentation Changes in version 0.99.12 o Support Bismark coverage file loading o Enhanced documentation and logging of loading steps o Minor bugfixes o Updates to the vignette and other documentation RnBeads 0.99.11 o Accommodate data packages for individual genomes o Performance: disk space usage when using disk dumping, options for subsetting sites when computing distance matrices for clustering, PCA and MDS o Region subsegmentation o The default method for differential methylation p-values is limma Changes in version 0.99.10 o Performance improvements o Option to keep big matrices on the hard drive rather than main memory o Restructuring of the filtering modules. Parts of the filtering steps are executed before normalization others afterwards o Improvements in normalization: more methods supported o Cosmetic changes to some of the plots Changes in version 0.99.9 o Bugfixes in paired analysis o Usability of bisulfite sequencing Changes in version 0.99.8 o New normalization methods integrated o Improved arguments to rnb.run.analysis o Improved parsing of the sample annotation table o Paired analysis (testing stage) o Webservice installed o Multiple bugfixes Changes in version 0.99.7 o Support for background subtraction and BMIQ normalization of Infinium 450k data o Support for differential methylation analysis on all pairs of sample groups Changes in version 0.99.6 o Locus Profiles o Support for parallel computing Changes in version 0.99.0 o Many additional features including bisulfite sequencing mode, the mouse genome, data export, ... Changes in version 0.5.0 o Initial release of RnBeads containing six modules - loading and normalization, quality control, filtering, batch effects, methylation profiles and differential methylation.