pRoloc 1.31

Changes in version 1.31.3

  • lopims() function moved to lgatto/lopims package on GitHub

Changes in version 1.31.2

  • Update dunkley2006params, andy2011params and MartInterfaces objects

Changes in version 1.31.1

  • Suggest magick (needed to build vignette)

Changes in version 1.31.0

  • New devel version (Bioc 3.13)

pRoloc 1.29

Changes in version 1.29.0

  • New devel version (Bioc 3.12)

Changes in version 1.29.1

  • Removed duplicate colour in getStockCol and updated the colour palette <Tue 2020-09-08>

pRoloc 1.28

Changes in version 1.28.0

  • New release version (Bioc 3.11)

pRoloc 1.27

Changes in version 1.27.6

  • Depend on MLInterfaces 1.67.10

Changes in version 1.27.5

  • import stats4::plot <2020-03-26 Thu>

Changes in version 1.27.4

Changes in version 1.27.3

  • Remove exprsToRatio man page (function in MSnbase and is deprecated)

Changes in version 1.27.2

  • Fix errors related to R-devel

Changes in version 1.27.1

  • Merged plotting payes PR

Changes in version 1.27.0

  • Version bump for Bioc 3.11 (devel)

pRoloc 1.25

Changes in version 1.25.3

  • New spatial2D function <2019-09-24 Tue>

Changes in version 1.25.2

  • Fix new biomart attribute <2019-08-09 Fri>
  • Bug fix: pass fcol to helper function (see https://support.bioconductor.org/p/123614/) <2019-08-09 Fri>

Changes in version 1.25.1

Changes in version 1.25.0

  • Version bump for Bioc 3.10 (devel)

pRoloc 1.24

Changes in version 1.24.0

  • Version bump for Bioc 3.9 (release)

pRoloc 1.23

Changes in version 1.23.4

  • Remove plain NEWS now that R supports NEWS.md

Changes in version 1.23.3

  • Link to TAGM F1000 workflow <2019-04-11 Thu>
  • Add ref to TAGM F1000 in CITATION and README <2019-04-11 Thu>
  • Update biomart interface data and AnnotationParams-related code <2019-04-12 Fri>

Changes in version 1.23.2

  • Add mcmc helper functions.
  • New logPosteriors accessor for MAPParams object.
  • New plotConsProfiles function, contributed by Tom Smith (see PR #131).
  • Update TAGM vignette, refering to workflow <2019-03-14 Thu>

Changes in version 1.23.1

  • Add note about missing data in QSep man <2018-10-31 Wed>
  • Add mcmc-helper documentation <2018-11-04 Sun>
  • Fixing numerical instability in Cholesky decomposition (see #124) <2018-11-30 Fri>
  • Add option to display or not display grid in plot2D <2018-12-12 Wed>
  • mrkHClust now uses mrkConsProfiles and returns the hclust object - see issue #130 for details and background <2018-12-19 Wed>

Changes in version 1.23.0

  • New version for Bioc 3.9 devel

pRoloc 1.22

Changes in version 1.22.0

  • New version for Bioc 3.8 release

pRoloc 1.21

Changes in version 1.21.9

  • Fix type in vignette header <2018-09-18 Tue>
  • Fix bug in plot method for ThetaRegRes object <2018-09-24 Mon>

Changes in version 1.21.8

  • Add an fcol argument to plotDist to plot and colour all profiles <2018-08-09 Thu>

Changes in version 1.21.7

  • Use BiocManager in vignette
  • Fix bug in plot2D: pass … to hexbin <2018-08-02 Thu>

Changes in version 1.21.6

  • Use BiocManager in installation instructions

Changes in version 1.21.5

  • Added new section in Bayesian spatial proteomics vignette detailing mcmc output processing <2018-07-07 Sat>

Changes in version 1.21.4

  • Fix bugs in tagmMcmcPredict, where fcol was ignored <2018-06-05 Tue>
  • Order vignettes by prefixing the files with numbers <2018-06-05 Tue>

Changes in version 1.21.3

  • New TAGM-MCMC generative model, contributed by Oliver Crook <2018-05-18 Fri>

Changes in version 1.21.2

  • Version bump for BiocStyle update: Vignette needed to be rebuilt to have bug fixed in BiocStyle footnote rendering.

Changes in version 1.21.1

  • Fix bug in higlightOnPlot with missing fcol (see #105) <2018-05-03 Thu>
  • New TAGM-MAP generative model, contributed by Oliver Crook <2018-05-18 Fri>
  • New plotEllipse function to visualise and assess TAGM models <2018-05-18 Fri>

pRoloc 1.20

Changes in version 1.20.0

  • New Bioconductor release 3.7

pRoloc 1.19

Changes in version 1.19.4

  • Fix regression bug in knntl function <2018-04-12 Thu>

Changes in version 1.19.3

  • Use dplyr::left_join without attaching dplyr to avoid collision between Biobase::exprs and dplyr::exprs <2018-04-04 Wed>.
  • Typo in warning to install rgl <2018-03-27 Tue>

Changes in version 1.19.2

  • Fix bug in QSep that prevented to set non-default fcol <2018-01-29 Mon>

Changes in version 1.19.1

  • Fix bug in private dimred and set appropriate number of colnames <2017-11-07 Tue>
  • New nipals method in dimensionality reduction for plot2D (closes issue #103) <2018-01-16 Tue>

Changes in version 1.19.0

  • Bioconductor devel 3.7

pRoloc 1.18

Changes in version 1.18.0

  • Bioconductor release 3.6

pRoloc 1.17

Changes in version 1.17.5

  • Filtering for unique features when running plot2D with t-SNE method <2017-10-15 Sun>

Changes in version 1.17.4

  • Added new (private) dimred function that computes dimensionality reduction <2017-06-05 Mon>
  • Add F1000research workflow to citations <2017-06-22 Thu>
  • Classification functions now return the classification score matrix for all classes as a single column in fData, rather that each class as its own fData column. <2017-09-01 Fri>

Changes in version 1.17.3

  • Convert vignettes to Rmd with html output <2017-05-25 Thu>
  • Import, rather than suggest Rtsne <2017-05-25 Thu>

Changes in version 1.17.2

  • phenoDisco speed improvements and added support for t-SNE <2017-05-19 Fri>

Changes in version 1.17.1

  • Support Rtsne’s new pca_center and pca_scale arguments <2017-05-02 Tue>

Changes in version 1.17.0

  • Version bump for Bioc devel 3.6