NEWS

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GeomxTools 3.7.3

• small bug fix in version comparisons (PKC & Seurat)
• update SpatialExperiment vignette plot coordinates

GeomxTools 3.7.2

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

GeomxTools 3.1.1

• Documentation correction

GeomxTools 3.1.0

• No changes from 2.99.2

GeomxTools 3.0.0

• No changes from 2.99.2
• Bioconductor release 3.15 version

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

GeomxTools 2.1.0

• No changes from 1.1.4

GeomxTools 2.0.0

• No changes from 1.1.4
• Bioconductor release 3.14 version

GeomxTools 1.99.4

• No changes from 1.1.4

GeomxTools 1.1.4

Revisions:

• Update license

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

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

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

GeomxTools 1.1.0

• No changes from 1.0.0

GeomxTools 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.

GeomxTools 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

GeomxTools 0.99.0

• Package template creation