An R package for quality metrics, preprocessing, visualization, and differential testing analysis of spatial omics data
Tutorial: https://github.com/riyuebao/nDSPA/wiki/Tutorial
Documentation: https://github.com/riyuebao/nDSPA/wiki/Documentation (under construction)
Short demo for the Rshiny app: https://bit.ly/3jpQh3e
To start using nDSPA.
- To launch the R shiny app on website:
-
Start using nDSPA!
- To launch the R shiny app locally:
-
download the software from
github
repository:git clone [email protected]:riyuebao/nDSPA.git
-
navigate into the
nDSPA
directory on your computer -
within the
nDSPA
directory, openapp.R
inRstudio
-
once
app.R
is open inRstudio
, clickRun App
button on the top right corner -
bravo! you are there
- To start using command line functions:
-
download the software from
github
repository:git clone [email protected]:riyuebao/nDSPA.git
-
navigate into the
nDSPA
directory on your computer -
source
global.R
nDSPA is under rapid development. Options might change between versions!
2020.08.28 Version 0.2a
- Added analysis and stats modules for data generated on NanoString DSP platform
- Added spatial expression map
- Added simulated test files
- Add multi-segment selection in QC and Normalization module
- Add R package support
- Add analysis modules and test files for data generated on Vectra mIF imaging platform
UPMC Hillman Cancer Center, supported in part by NCI through the UPMC Hillman Cancer Center CCSG award (P30CA047904).”
We acknowledge contribution from our colleagues and friends in pushing nDSPA to fuition:
- We thank Shelley Reynolds and Ernest M Meyer (UPMC Flow Cytometry Core) for processing the samples and producing the data that were used to generate the syntethic datasets provided in nDSPA.
- We thank Aditi Kulkarni (UPMC Hillman Cancer Center), Kyle Hernandez, Tzuni Garcia and Lei Huang (University of Chicago) for helping test and verify the software.
Rajesh Acharya, Tullia Bruno, Jason J Luke, and Riyue Bao. nDSPA: An R package for quality metrics, preprocessing, visualization, and differential testing analysis of spatial omics data. Link: https://github.com/riyuebao/nDSPA
Please reach out to us by emails, leave us a message here, or find us on twitter!
Please submit a ticket on GitHub issues.