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# escheR <!-- badges: start --> R Package Status: [![Lifecycle: stable](]( [![R build status](]( Bioc Status: [![Bioc release status](]( [![Bioc devel status](]( [![Bioc history](]( [![Bioc last commit](]( <!-- badges: end --> The goal of escheR is to create an unified multi-dimensional spatial visualizations for spatially-resolved transcriptomics data following Gestalt principles. ![](man/figures/insitu.jpg) Our preprint describing the innovative visualization is available from [bioRxiv]( # Installation You can install the latest release version of `escheR` from Bioconductor. with using the following code will install version of the `nnSVG` package from Bioconductor. Additional details are shown on the [Bioconductor]( page. ```{r install_bioc, eval=FALSE} if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("escheR") ``` The latest development version can also be installed from the `devel` version of Bioconductor or from [GitHub]( following ```{r install_github, eval = FALSE} if (!require("devtools")) install.packages("devtools") devtools::install_github("boyiguo1/escheR") ``` If you have R version before v4.3 and would like to install `escheR`, you can follow ```{r pre-R4.3, eval = FALSE} if (!require("devtools")) install.packages("devtools") devtools::install_github("boyiguo1/escheR@pre-R4.3") ``` > WARNING: The purpose of having the branch `pre-R4.3` is to allow users to use `escheR` before the formal release of R 4.3 and during the early stage of R 4.3 release. This branch will not update with any further development passing [`escheR v0.99.6`]( We recommend users to update their R versions up to date. # Input data format To use `escheR`, we assume the input data are provided as a [`SpatialExperiment`]( Bioconductor object. For people whose data are stored as a [`Seurat`]( object, we advise to convert to a `SpatialExperiment` object before applying the workflow below. # Tutorial Please find an end-to-end tutorial at []( # Citation Our preprint describing `escheR` is available from bioRxiv: * Guo B, Hicks SC (2023). “escheR: Unified multi-dimensional visualizations with Gestalt principles.” _bioRxiv_. doi:10.1101/2023.03.18.533302 # Acknowledgement ## Development tools - Continuous code testing is possible thanks to [GitHub actions]( through *[biocthis](*, - The [documentation website]( is automatically updated thanks to *[pkgdown](*. - The code is styled automatically thanks to *[styler](*. - The documentation is formatted thanks to *[devtools](* and *[roxygen2](*.