Changes in version 3.6.2                        

  - Seurat v5 coercion
  - IPA data loading
  - improved Proteogenomics error handling
  - bug fix on area filtering

                        Changes in version 3.1.1                        

  - Documentation correction

                        Changes in version 3.1.0                        

  - No changes from 2.99.2

                        Changes in version 3.0.0                        

  - No changes from 2.99.2
  - Bioconductor release 3.15 version

                       Changes in version 2.99.2                        

  - documentation updates

                       Changes in version 2.99.1                        

  - documentation updates

                        Changes in version 2.1.9                        

  - documentation updates

                        Changes in version 2.1.8                        

  - subset objects in tests & examples to decrease time

                        Changes in version 2.1.7                        

  - coercions to Seurat and SpatialExperiment are S3 coercions

                        Changes in version 2.1.6                        

  - added updateObject capability

                        Changes in version 2.1.5                        

New features:

  - Handle multiple PKC file versions for a single module
      - Only common probes in all versions for each module will be used
      - Default behavior most recent PKC version for resolving probe
        assignments
      - User can override default with a specified version file name
  - Added SystematicName and GeneID from PKC to feature metadata

                        Changes in version 2.1.4                        

  - Add code for grubbs test from deprecated outliers package

                        Changes in version 2.1.3                        

New features:

  - Allow protein NGS experiment data reading
      - New slot, analyte, added to refer to analyte type

                        Changes in version 2.1.2                        

Bug fixes:

  - Bug fix in outlier testing

                        Changes in version 2.1.1                        

New features:

  - Add coercion to Seurat and SpatialExperiment

                        Changes in version 2.1.0                        

  - No changes from 1.1.4

                        Changes in version 2.0.0                        

  - No changes from 1.1.4
  - Bioconductor release 3.14 version

                       Changes in version 1.99.4                        

  - No changes from 1.1.4

                        Changes in version 1.1.4                        

Revisions:

  - Update license

                        Changes in version 1.1.3                        

Revisions:

  - Allow for multipanel background correction in subtractBackground()
  - Allow user to re-run summarizeNegatives()
  - Enable optional parameters in readNanoStringGeoMxSet() for
    annotation file reading
  - Added and revised test cases throughout

Bug fixes:

  - Fixed writeNanoStringGeoMxSet to work with current DCC file format

                        Changes in version 1.1.2                        

Revisions:

  - Allow users to use more than one DCC version
  - Speed improvements in setBioProbeQC() and aggregateCounts()

Bug fixes:

  - Fix error in setBioProbeQC() with single panel objects
  - Fix mixed model output to reference correct p-value
  - Fix thresholding in utility functions to keep format matrix format
    inputs

                        Changes in version 1.1.1                        

New features:

  - Differential expression with linear mixed model method
    mixedModelDE()

Revisions:

  - Handle multi-panel normalization

Bug fixes:

  - Fix skipping of vectors that don't meet Grubbs requirements
  - Fix build warning from knitr update

                        Changes in version 1.1.0                        

  - No changes from 1.0.0

                        Changes in version 1.0.0                        

  - Initial release, includes load with automatic aggregation to
    target-level

User notes:

  - This version was included in Bioconductor release 3.13

Citation:

Ortogero, N.; Yang, Z.; Vitancol, R.; Griswold, M.; Henderson, D.
GeomxTools: NanoString GeoMx Tools. R Package Version 1.0.0. NanoString
Technologies Inc.; Seattle, WA 98109, USA. 2021.

                       Changes in version 0.99.4                        

v0.99.4 includes changes beyond 1.0.0

New features:

  - New slot FeatureType to indicate if data is probe- or target-level
  - Segment QC setSegmentQCFlags() and probe QC setBioProbeQC()
  - Count aggregation method aggregateCounts()
  - Common GeoMx normalizations normalize()
  - Log and count thresholding methods added to utils

Revisions:

  - Updated readDccFile() to expand dcc file versions accepted
  - Allow user to without auto-aggregating counts to target-level
  - Probe annotations attached to featureData with readPKCFile

                       Changes in version 0.99.0                        

  - Package template creation