Package: bgnormR 0.99.5

Dharmesh D. Bhuva

bgnormR: Background Normalisation for Multiplex Spatial Proteomics

Implements bgnorm, a generative statistical framework for background correction, normalisation, and quality control in multiplex spatial proteomics. The method models fluorescence pixel intensities as a three-component mixture of log-normal convolutions representing background, non-specific binding, and biological signal. A deconvolution step separates the signal component from background sources, and a model-based quantile normalisation (bgnormQ) unifies measurements across markers, samples, and three-dimensional tissue slices. A Jensen-Shannon Divergence metric provides automated quality control. A Java-free reader for Akoya PhenoCycler-Fusion QPTIFF, OME-TIFF, and OME-Zarr (OME-NGFF) images is included.

Authors:Dharmesh D. Bhuva [aut, cre], Rafael Tubelleza [aut], Malvika Kharbanda [aut], Agus Salim [aut]

bgnormR_0.99.5.tar.gz
bgnormR_0.99.5.zip(r-4.7-any)bgnormR_0.99.5.zip(r-4.6-any)bgnormR_0.99.5.zip(r-4.5-any)
bgnormR_0.99.5.tgz(r-4.6-any)bgnormR_0.99.5.tgz(r-4.5-any)
bgnormR_0.99.5.tar.gz(r-4.7-any)bgnormR_0.99.5.tar.gz(r-4.6-any)
bgnormR_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bgnormR/json (API)

# Install 'bgnormR' in R:

install.packages('bgnormR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bhuvalab/bgnormr/issues

On CRAN:

normalization preprocessing singlecell spatial proteomics immunooncology qualitycontrol dataimport

3.30 score 5 scripts 29 exports 75 dependencies

Last updated from:b187a5be69. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	224
linux-devel	OK	278
source / vignettes	OK	307
linux-release	OK	338
macos-release	OK	267
macos-oldrel	OK	252
windows-devel	OK	235
windows-release	OK	298
windows-oldrel	OK	286
wasm-release	OK	145

Exports:as.QPTIFFImage bgnorm_cells bgnorm_pixels bgnorm_results bgnorm_sce channel_table extract_array inv_log_transform jsd_gaussians jsd_qc log_transform median_filter_3x3 metadata plot_distributions plot_jsd_heatmap plot_pixel_classes plot_qptiff qc_summary qpi_channel_names qpi_channels qpi_format qpi_is_brightfield qpi_n_levels qpi_pixel_size_um qpi_primary_scene read_qptiff show type write_qptiff

Dependencies:abind askpass BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob cachem cli codetools cpp11 curl DBI dbplyr DelayedArray dplyr farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable httr2 IRanges isoband labeling lambda.r lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats mclust memoise openssl pillar pkgconfig purrr R6 RColorBrewer Rcpp rjson rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

Getting started with bgnormR

Rendered frombgnormR.Rmdusingknitr::rmarkdown

Last update: 2026-11-08
Started: 2026-07-01

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

Package: bgnormR 0.99.5

bgnormR: Background Normalisation for Multiplex Spatial Proteomics

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)