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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# MoleculeExperiment <img src="https://github.com/raw/SydneyBioX/SydneyBioXStickers/main/MoleculeExperiment/MoleculeExperiment.png" align="right" width=250 style="margin-left: 10px;">
<!-- badges: start -->
[![name](https://img.shields.io/badge/BIOCONDUCTOR%20TUTORIAL-%23001F3F)](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 (accepted)
[![Static Badge](https://img.shields.io/badge/PREPRINT-darkgreen)](https://www.biorxiv.org/content/10.1101/2023.05.16.541040v1#:~:text=MoleculeExperiment%20enables%20consistent%20infrastructure%20for,transcriptomics%20data%20in%20Bioconductor%20%7C%20bioRxiv)