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Bioconductor - jazzPanda

jazzPanda

This is the released version of jazzPanda; for the devel version, see jazzPanda.

Finding spatially relevant marker genes in image based spatial transcriptomics data

Bioconductor version: Release (3.21)

This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.

Author: Melody Jin [aut, cre] ORCID: 0000-0002-2222-0958

Maintainer: Melody Jin <jin.m at wehi.edu.au>

Citation (from within R, enter citation("jazzPanda")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("jazzPanda")

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("jazzPanda")

Details biocViews DifferentialExpression, GeneExpression, Software, Spatial, StatisticalMethod, Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License GPL-3 Depends R (>= 4.5.0) Imports spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr, doParallel, BiocParallel, methods, BumpyMatrix, SpatialExperiment System Requirements URL https://github.com/phipsonlab/jazzPanda https://bhuvad.github.io/jazzPanda/ Bug Reports https://github.com/phipsonlab/jazzPanda/issues See More Suggests BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod, corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2, igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr, SpatialFeatureExperiment, ExperimentHub, TENxXeniumData, SingleCellExperiment, SFEData, Matrix, data.table, scran, scater, grid, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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