Package: SpaNorm 1.1.0

Dharmesh D. Bhuva

SpaNorm: Spatially-aware normalisation for spatial transcriptomics data

This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

Authors:Dharmesh D. Bhuva [aut, cre], Agus Salim [aut], Ahmed Mohamed [aut]

SpaNorm_1.1.0.tar.gz
SpaNorm_1.1.0.zip(r-4.5)SpaNorm_1.1.0.zip(r-4.4)
SpaNorm_1.1.0.tgz(r-4.4-any)
SpaNorm_1.1.0.tar.gz(r-4.5-noble)SpaNorm_1.1.0.tar.gz(r-4.4-noble)
SpaNorm_1.1.0.tgz(r-4.4-emscripten)
SpaNorm.pdf |SpaNorm.html✨
SpaNorm/json (API)
NEWS

# Install 'SpaNorm' in R:

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

Bug tracker:https://github.com/bhuvad/spanorm/issues

Pkgdown:https://bhuvad.github.io

Datasets:

HumanDLPFC - Human dorsolateral prefrontal cortex (DLPFC) visium sample

On BioConductor:SpaNorm-1.1.0(bioc 3.21)SpaNorm-1.0.0(bioc 3.20)

software geneexpression transcriptomics spatial cellbiology

5.77 score 9 stars 3 scripts 4 exports 117 dependencies

Last updated 2 months agofrom:6bf7b580af. Checks:OK: 1 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	NOTE	Nov 30 2024
R-4.5-linux	NOTE	Nov 30 2024
R-4.4-win	NOTE	Nov 30 2024
R-4.4-mac	NOTE	Nov 30 2024

Exports:fastSizeFactors filterGenes plotSpatial SpaNorm

Dependencies:abind askpass assorthead beachmat BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel BiocSingular bit bit64 blob bluster cachem cli cluster codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray digest dotCall64 dplyr dqrng edgeR fansi farver fastmap filelock formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue gtable httr igraph IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle limma listenv locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mgcv mime munsell nlme openssl parallelly pillar pkgconfig plogr progressr purrr R6 RColorBrewer Rcpp RcppEigen rjson rlang RSQLite rsvd S4Arrays S4Vectors ScaledMatrix scales scran scuttle SeuratObject SingleCellExperiment sitmo snow sp spam SparseArray SpatialExperiment statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

SpaNorm: Spatially aware library size normalisation

Dharmesh D. Bhuva and Agus Salim

Rendered fromSpaNorm.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2024-10-13
Started: 2024-05-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filter genes based on expression	fastSizeFactors fastSizeFactors,SpatialExperiment-method
Filter genes based on expression	filterGenes filterGenes,Seurat-method filterGenes,SpatialExperiment-method
Human dorsolateral prefrontal cortex (DLPFC) visium sample	HumanDLPFC
Plot spatial transcriptomic annotations per spot	plotSpatial
Spatially-dependent normalisation for spatial transcriptomics data	SpaNorm SpaNorm,SpatialExperiment-method
An S4 class to store a SpaNorm model fit	$,SpaNormFit-method SpaNormFit SpaNormFit-class