prepareSpatialDecon() to convert the selected log2 assay to linear
expression by default, preserving its normalization or batch correction.
Add isLog for linear inputs and recomputeCPM to recompute linear CPM
from raw counts with matching negative-probe scaling. Raw metadata probes
now require recomputation or raw-count input rather than an independently
normalized background.stats::setNames() to avoid R CMD check notes.readGeoMxFromDcc() importer for DCC/PKC workflows and
remove GeomxTools from Suggests.GeomxTools to Suggests so examples using
readGeoMxFromNanoStringGeoMxSet() can run in coverage workflows.Add readGeoMxFromNanoStringGeoMxSet() to convert
GeomxTools::readNanoStringGeoMxSet() / NanoStringGeoMxSet objects from
DCC/PKC workflows into SpatialExperiment objects for standR.
Improve prepareSpatialDecon() so negative probes removed by
readGeoMx(rmNegProbe = TRUE) can be read from metadata(spe)$NegProbes.
Add function prepareSpatialDecon to help using R package SpatialDecon after using standR to preprocess GeoMx data.
New RUV-4: now using the RUV-4 from standR allow you to perform rank-based analysis such as gene-set scoring with the RUV-4-normalised count.
New vignette - A quick start guide to the standR package.
Many bugs fixed.