Skip to content

Latest commit

 

History

History
91 lines (54 loc) · 2.64 KB

NEWS.md

File metadata and controls

91 lines (54 loc) · 2.64 KB

InSituType 2.0.0

  • Enable use in protein datasets via the assay_type argument. This required a major overhaul under the hood, but has little impact on existing RNA workflows.
  • More advanced methods for updating reference profiles via anchor cells, implemented in updateReferenceProfiles.
  • New function spatialUpdate for using alternative data types (e.g. space or immunofluorescence) and the Insitutype likelihood framework to update cell typing results from any method.
  • New function getSpatialContext for conveniently calculating cells' spatial contexts / neighborhood expression.
  • New functions getRNAprofiles and getProteinParameters, which serve as user-facing tools for getting profile matrices.

InSituType 1.2.3

  • handle collinearity issues with fastCohorting: Reduce to 2 PC's. If this fails, then try successively smaller # of cohorts with the 2 pc's.

InSituType 1.2.2

  • Add Compatibility of assay_type and platform effect correction

InSituType 1.2.1

  • Create "undefined" profile for cells with zero counts

InSituType 1.2.0

  • Also cluster continuous data from protein assay

InSituType 1.1.1

  • Support platform effect correction
  • Support anchor refinement via UMAP projection

InSituType 1.1.0

  • Support matrices with more than 4B elements

InSituType 1.0.0

  • License updated
  • lldist parallelized with OpenMP

InSituType 0.99.4

  • Re-submission to Bioconductor

InSituType 0.99.3

  • Merge subclustering fix

InSituType 0.99.2

  • Optionally use SingleCellExperiment class

InSituType 0.99.1

  • Added reference to CosMx paper and dataset

InSituType 0.99.0

  • Submission to Bioconductor 3.16

InSituType 1.1.1

  • Updated flightpath_layout.R to save the plot in a temp folder in the current work directory

InSituType 1.1.0

  • Fix several places counts matrix was being converted to dense to calculate a statistic
    • Revert conversion to sparse matrix of dense mu matrix and result from dnbinom

InSituType 1.0.0

  • Integrated rcpp support for the package
  • Added dnbinom for sparse matrices
  • Updated the unit tests
  • Removed .o files in src folder

InSituType 0.1.2

  • Updated package dependencies

InSituType 0.1.1

  • Added lsa, SpatialDecon, irlba, mclust, rmarkdown to the DESCRIPTION file
  • Fixed a Roxygen example for the R function geoSketch where it was trying to use Ptolemy and Giotto packages that are not being used within the package

InSituType 0.1.0

  • Added a NEWS.md file to track changes to the package.
  • Added BioConductor package dependencies (notably SpatialDecon and lsa)
  • Renamed vignettes to allow for compilation
  • Deleted old vignettes (labelled OLD)