Shiny app for the exploration and analysis of single cell RNAseq data as it comes from 10X or MARSseq technologies. It is currently being developed based on user requests of the Cytometry and Biomarkers UTechS at the Pasteur Institute, Paris. The goal is to enable the users of our platform to explore their data, select cells they would like to work with and then perform the final analysis together with the bioinformatics support at Pasteur.
Developper tools need to be installed please see for further information:
update.packages() if (!require("devtools")) install.packages("devtools") # devtools::install_github("mul118/shinyMCE") if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # update bioconductor packages if required BiocManager::install() # BiocManager::install("BiocSingular") BiocManager::install("SingleR") # needed to prepare data. devtools::install_github("haowulab/Wind") devtools::install_github("C3BI-pasteur-fr/UTechSCB-SCHNAPPs", dependencies = TRUE)
To take advantage of the history functionality orca needs to be installed: (https://github.com/plotly/orca#installation)
orca is part of ploty so nothing to be done for R. But the pdftools are required:
Load a small set of 200 PBMC cells and save to a file in the local directory. This file can be uploaded using the app.
To start the app:
Plots can be automatically stored in a PDF file as they are created. This allows to somehow track what is being done. To enable this, the parameter historyFile has to be set to a file (probably non-existing, otherwise it will be appended to).
A singleCellExperiment object is required, saved in a file RData object using
Please see GitHub for further documentation on how to use schnapps.
Please see GitHub Contributions for additional tools, not directly part of the SCHNAPPs pacakage.
See SCHNAPPsContribution for examples and dummy contributions on how add functionality.
The original version of this app is based on CellView (https://github.com/mohanbolisetty/CellView), but it was substantially modified. It helped me get started.
We are also greatful to all the members of the single cell working group at Pasteur Paris.