# iSEEfier <!-- badges: start --> [](https://github.com/NajlaAbassi/iSEEfier/actions/workflows/R-CMD-check.yaml) <!-- badges: end --> The goal of `iSEEfier` is to provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects for the `iSEE` package. These can be conveniently passed in a straightforward manner to the function call to launch `iSEE()` with the specified configuration, tailored to individual visualisation objectives. This package currently works seamlessly with the sets of panels provided by the `iSEE` and `iSEEu` packages, but can be extended to accommodate the usage of any custom panel (e.g. from `iSEEde`, `iSEEpathways`, or any panel developed independently by the user). `iSEEfier` can be found on Bioconductor (<https://www.bioconductor.org/packages/iSEEfier>). ## Installation You can install the development version of `iSEEfier` from GitHub with: ``` r library("remotes") remotes::install_github("NajlaAbassi/iSEEfier", dependencies = TRUE, build_vignettes = TRUE) ``` ## Example This is a basic example which shows you how to use `iSEEfier` on a demo dataset (the one included in the `scRNAseq` package). ``` r library(iSEEfier) library(iSEE) sce <- scRNAseq::RichardTCellData() sce <- scuttle::logNormCounts(sce) sce <- scater::runPCA(sce) sce <- scater::runTSNE(sce) gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437") cluster <- "stimulus" group <- "single cell quality" initial <- iSEEinit(sce = sce, features = gene_list, clusters = cluster, groups = group) iSEE(sce, initial = initial) ``` ## Usage overview You can find the rendered version of the documentation of `iSEEfier` at the project website <https://NajlaAbassi.github.io/iSEEfier>, created with `pkgdown`. ## Development If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an [issue](https://github.com/NajlaAbassi/iSEEfier/issues). ## Code of Conduct Please note that the iSEEfier project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms. ## License MIT