Package index • bgnormR

All functions

BgnormResult: BgnormResult S3 class
dim(<OMEZarrArraySeed>) dimnames(<OMEZarrArraySeed>) type(<OMEZarrArraySeed>) extract_array(<OMEZarrArraySeed>): Seed class for lazy on-disk OME-Zarr access
dim(<QPTIFFArraySeed>) dimnames(<QPTIFFArraySeed>) type(<QPTIFFArraySeed>) extract_array(<QPTIFFArraySeed>): Seed class for lazy on-disk QPTIFF access
QPTIFFImage: QPTIFFImage: an in-memory or on-disk multi-channel image
QPTIFFMetadata: QPTIFFMetadata: an OME-organised image metadata object
as.QPTIFFImage(): Coerce a 3-D array to a QPTIFFImage
as.array(<QPTIFFImage>): Materialise a QPTIFFImage to a plain 3-D array
as.list(<QPTIFFImage>): Convert a QPTIFFImage to a named list of 2-D channel matrices
as.matrix(<QPTIFFImage>): Coerce a single-channel QPTIFFImage to a matrix
bgnormR-package bgnormR: bgnormR: Background Normalisation for Multiplex Spatial Proteomics
bgnorm_cells(): Cell-level background normalisation (bgnorm)
bgnorm_pixels(): Pixel-level background normalisation (bgnorm) for a QPTIFFImage
bgnorm_results(): Per-channel bgnorm results stored in a QPTIFFImage
bgnorm_sce(): Apply cell-level bgnorm to a SingleCellExperiment or matrix
channel_table(): Tidy per-channel metadata table
`dimnames<-`(<QPTIFFImage>): Replace the dimnames of a QPTIFFImage
inv_log_transform(): Inverse log2 transform with cofactor
jsd_gaussians(): Jensen-Shannon Divergence between two Gaussian distributions
jsd_qc(): Compute the JSD quality control metric from bgnorm model parameters
length(<QPTIFFImage>): Number of channels in a QPTIFFImage
log_transform(): Log2 transform with cofactor
median_filter_3x3(): Apply a 3 x 3 median filter to a matrix
metadata(): Access the metadata embedded in a QPTIFFImage
`names<-`(<QPTIFFImage>): Set the channel names of a QPTIFFImage
names(<QPTIFFImage>): Channel names of a QPTIFFImage (third-dimension names of the array)
plot_distributions(): Per-marker intensity distribution with fitted GMM densities
plot_jsd_heatmap(): QC heatmap of Jensen-Shannon Divergence across markers and samples
plot_pixel_classes(): Spatial GMM class assignment plot for a QPTIFFImage or SpatialExperiment
plot_qptiff(): Spatial intensity plot for a QPTIFFImage or SpatialExperiment
qc_summary(): Summarise QC across multiple bgnorm results
qpi_channel_names(): Channel names of the primary scene
qpi_channels(): Per-channel metadata of the primary scene
qpi_format(): Acquisition format of a parsed image
qpi_is_brightfield(): Is the primary scene a brightfield (RGB) image?
qpi_n_levels(): Number of pyramid levels of the primary scene
qpi_pixel_size_um(): Physical pixel size (microns) of the primary scene, full resolution
qpi_primary_scene(): Primary scene of a parsed image (FullResolution if present, else the first)
read_qptiff(): Read a multiplex image (QPTIFF, OME-TIFF, or OME-Zarr)
`[`(<QPTIFFImage>): Subset a QPTIFFImage
write_qptiff(): Write a QPTIFFImage to a TIFF file