# MoleculeExperiment \[!\[name\](https://img.shields.io/badge/BIOCONDUCTOR%20TUTORIAL-%23001F3F)\](https://bioconductor.org/packages/release/bioc/vignettes/MoleculeExperiment/inst/doc/MoleculeExperiment.html) 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 \[!\[Static Badge\](https://img.shields.io/badge/LINK%20TO%20PAPER-darkgreen)\](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad550/7271181)
\[!\[name\](https://img.shields.io/badge/BIOCONDUCTOR%20TUTORIAL-%23001F3F)\](https://bioconductor.org/packages/release/bioc/vignettes/MoleculeExperiment/inst/doc/MoleculeExperiment.html) 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 \[!\[Static Badge\](https://img.shields.io/badge/LINK%20TO%20PAPER-darkgreen)\](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad550/7271181)