Changes in version 3.7.2 - 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