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.