v2.99.2

GeomxTools 2.99.2

• documentation updates

GeomxTools 2.99.1

• documentation updates

GeomxTools 2.1.9

• documentation updates

GeomxTools 2.1.8

• subset objects in tests & examples to decrease time

GeomxTools 2.1.7

• coercions to Seurat and SpatialExperiment are S3 coercions

GeomxTools 2.1.6

• added updateObject capability

GeomxTools 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

GeomxTools 2.1.4

• Add code for grubbs test from deprecated outliers package

GeomxTools 2.1.3

New features:

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

GeomxTools 2.1.2

Bug fixes:

• Bug fix in outlier testing

GeomxTools 2.1.1

New features:

• Add coercion to Seurat and SpatialExperiment

Pre-release version 1.99.4

GeomxTools 1.99.4

• No changes from 1.1.4

Pre-release version 1.1.4

GeomxTools 1.1.4

Revisions:

• Update license

Pre-release version 1.1.3

GeomxTools 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

Pre-release version 1.1.2

GeomxTools 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

Pre-release version 1.1.1

GeomxTools 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

v0.99.4-beta

Pre-release version that has gone through Verification and Validation in PI-9
This is the version that is included in the stabilization build for DSPDA v2.4

Features Included in the V&V:
Loading
Sequencing QC (same defaults as DSPDA)
Probe QC
Normalization (without the multiple panel neg normalization)