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Commits on Sep 26, 2018

• fixed an issue for handling RnBDiffMeth objects with no regions

  demuellae

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• added GOstats reference to RnBeads reports

  demuellae

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Commits on Sep 25, 2018

• Set a reference to Pidsley et al. 2016 to the Preprocessing report when filtering cross-reactive probes.

  yxomo

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• Added one sentence to the description of the LUMP values in the report on Covariate Inference.

  yxomo

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Commits on Sep 24, 2018

• more tooltips in RnBeadsDJ

  demuellae

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Commits on Sep 23, 2018

• RnBeadsDJ: tooltips for tabs and parameter selection elements

  demuellae

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Commits on Sep 22, 2018

• Fix reviewer comment: number of cores now only gets set when (parts of) the analysis is run

  demuellae

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Commits on Sep 12, 2018

• Merge branch 'feature/RnBeads2.0' of github.com:epigen/RnBeads into feature/RnBeads2.0

  schmic05

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• Updated NEWS

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• Changes all occurences of 'gender' to the more neutral word 'sex'

  schmic05

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Commits on Aug 30, 2018

• replace BiocInstaller biocLite mentions with BiocManager

  LiNk-NY

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Commits on Aug 1, 2018

• Merge branch 'feature/RnBeads2.0' of github.com:epigen/RnBeads into feature/RnBeads2.0

  schmic05

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• Updated news and version bump

  schmic05

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• Fixed rnb.region.types if an object names mm10, hg19, etc. is present in the environment

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Commits on Jul 27, 2018

• Small modifications to the color legends displayed next to heatmaps.

  yxomo

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Commits on Jul 24, 2018

• Changed defaults in 'data.frame2GRanges' to the ones used in the 'annotation' function

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Commits on Jul 23, 2018

• Changed CNV reference to newest version

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• Fixed CNV plotting in the case no breakpoints exist

  schmic05

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Commits on Jul 20, 2018

• Reduced number of breakpoints in CNV estimation

  schmic05

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• Fixed bug in RnBeadSet constructor if duplicate probe ids exist

  schmic05

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• Fixed bug in CNV plotting

  schmic05

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Commits on Jul 19, 2018

• Fixed crashing of QC in detached screen (X11 not available)

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  schmic05

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• Converted QC and Preprocessing to sequential execution in the cluster computation

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Commits on Jul 17, 2018

• Merge branch 'feature/cnv_estimation' into feature/RnBeads2.0

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• Added parallel plotting utils

  schmic05

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Commits on Jul 13, 2018

• Fixed small typo in logging

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• Presumably increased performance of CNV estimation

  schmic05

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• Fixed type on options

  schmic05

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• Fixed imputation of one-sample datasets

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• Added more info to the report

  schmic05

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• Fixed CNV for RnBiseq

  schmic05

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• Fixed typo in CNV options

  schmic05

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• Minor modifications

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Commits on Jun 29, 2018

• Added support for old RnBeads.hg19 version

  schmic05

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• Added first working version of CNV estimation, new options are qc.cnv and qc.cnv.refbased

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