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RnBeads 2.19.0
=============
* Fixed issue with logical having a length greater than 1
RnBeads 2.17.1
=============
* Temporarily removed the GLAD dependency and CNV functionality
RnBeads 2.17.0
=============
* Fixed bug in differential variability analysis
RnBeads 2.15.1
=============
* Added custom reimplementations of dye-bias and background correction methods from SeSaMe
RnBeads 2.13.2
=============
* Removed support for RefFreeEWAS, since the package is not supported anymore
RnBeads 2.13.0
=============
* Compatibility fixes with SeSaMe by zwdzwd
* Minor bugfixes
RnBeads 2.11.0
=============
* Bugfixes in MMBC support
RnBeads 2.9.4
=============
* Added initial version of the Mouse Methylation Bead Chip support
* Native implementations of basic dye-bias and background correction methods (methylumi dependency removed)
RnBeads 2.9.3
=============
* Changed some of the default options values
* Some bugfixes
RnBeads 2.9.2
=============
* Implemented function rnb.execute.pOOBAH. Thanks to Nathan Steenbuck.
* Update of contact information in DESCRIPTION
RnBeads 2.9.1
=============
* Improved function intensities.by.color. Thanks to Nathan Steenbuck.
RnBeads 2.7.1
=============
* Added conversion from RnBeadRawSet to RGChannelSet
RnBeads 2.3.3
=============
* Fixed non ASCII column names in age prediction and immune estimation
RnBeads 2.3.2
=============
* Added stratification plots for inferred covariates in different sample groups
RnBeads 2.1.3
=============
* Implemented methylation based segmentation by the MethylSeekR approach. Thanks to Abdulrahman Salhab for providing code for the integration.
* Wrapper for load.rnb.set
RnBeads 2.1.2
=============
* Fix in as.RnBeadRawSet
* Added new paper to CITATION
RnBeads 2.1.1
=============
* Added support for SLURM compute cluster architecture
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.