<!-- README.md is generated from README.Rmd. Please edit that file --> # MoleculeExperiment <img src="https://raw.githubusercontent.com/SydneyBioX/SydneyBioXStickers/main/MoleculeExperiment/MoleculeExperiment.png" align="right" width=250 style="margin-left: 10px;"> <!-- badges: start --> [](https://bioconductor.org/packages/release/bioc/vignettes/MoleculeExperiment/inst/doc/MoleculeExperiment.html) <!-- badges: end --> The goal of MoleculeExperiment is to provide functionality for the representation and summarisation of imaging-based spatial transcriptomics data, including 10X Xenium. MoleculeExperiment will take you from machine output data directly to an object ready for analyses! 🚀 We used the following data bundles to inform our readXenium, readCosmx and readMerscope functions respectively. In particular, Xenium data corresponds to [3 replicates from fresh frozen mouse brain tissue](https://www.10xgenomics.com/resources/datasets/fresh-frozen-mouse-brain-replicates-1-standard), accessed on 8 February 2023; CosMx data corresponds to [human non-small cell lung cancer](https://nanostring.com/resources/smi-ffpe-dataset-lung9-rep1-data/) accessed on 27 February 2023; and MERSCOPE data is from [human ovarian cancer](https://console.cloud.google.com/storage/browser/vz-ffpe-showcase/HumanOvarianCancerPatient2Slice2) accessed on 27 February 2023. ## Installation You can install the development version of MoleculeExperiment from [GitHub](https://github.com/) with: ``` r # install.packages("devtools") devtools::install_github("SydneyBioX/MoleculeExperiment") ``` ### System dependencies Note that the following 3 system dependencies are required: \* libssl-dev \* libmagick++-dev \* libgdal-dev ### Citation Peters Couto et al, 2023, Bioinformatics [](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad550/7271181)