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NEWS.md

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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 0.99.4 - concomittant development branch version

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 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 0.99.0

  • Package template creation