spammR

This is the development version of spammR; to use it, please install the devel version of Bioconductor.

SPatial Analysis of Multiomics Measurements in R

Bioconductor version: Development (3.24)

SpammR provides a suite of tools and a data structure to analyze diverse multiomics measurements in a spatial context. It enables the analysis and visualization of omics measurements paired with a specific image, each with spatial coordinates.

Author: Sara Gosline [cre, aut] ORCID: 0000-0002-6534-4774 , Harkirat Sohi [aut] ORCID: 0009-0000-9935-1641 , Yannick Mahlich [aut] ORCID: 0000-0002-0717-2927

Maintainer: Sara Gosline <sara.gosline at pnnl.gov>

Citation (from within R, enter citation("spammR")):

Sara Gosline, Harkirat Sohi, Yannick Mahlich. spammR: SPatial Analysis of Multiomics Measurements in R. doi:10.18129/B9.bioc.spammR, R package version 0.99.26, https://bioconductor.org/packages/spammR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("spammR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("spammR")

spammR-lipids	HTML	R Script
spammR-microbes	HTML	R Script
spammR-protein	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, Cheminformatics, Clustering, Coverage, DataImport, DifferentialExpression, DifferentialSplicing, Epigenetics, ExonArray, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Metabolomics, MicroRNAArray, Microarray, MultipleComparison, Normalization, OneChannel, Pathways, Preprocessing, ProprietaryPlatforms, Proteomics, QualityControl, RNASeq, Regression, Sequencing, SingleCell, Software, Spatial, SystemsBiology, TimeCourse, Transcription, Transcriptomics, TwoChannel, mRNAMicroarray
Version	0.99.26
In Bioconductor since	BioC 3.24 (R-4.6)
License	MIT + file LICENSE
Depends	SummarizedExperiment, SingleCellExperiment, SpatialExperiment, limma, R (>= 4.5.0)
Imports	dplyr, ggplot2, plotly, ggnewscale, ggpubr, png, reticulate, impute, matrixStats, scales, spdep, ggrepel, IRanges, tibble, tidyr, leapR, tidygraph, ggraph, BiocFileCache, terra, readxl, tidygraph, tidyverse, magrittr, sf, cowplot, DT
System Requirements	python = 3.11
URL	https://pnnl-compbio.github.io/spammR/
Bug Reports	https://github.com/PNNL-CompBio/spammR/issues

Suggests	testthat (>= 3.0.0), BiocStyle, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	spammR_0.99.26.tar.gz
Windows Binary (x86_64)	spammR_0.99.26.zip
macOS Binary (big-sur-x86_64)	spammR_0.99.26.tgz
macOS Binary (sonoma-arm64)	spammR_0.99.26.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spammR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spammR
Package Short Url	https://bioconductor.org/packages/spammR/
Package Downloads Report	Download Stats