Application - Single Cell Mass Cytometry Harmonization Tool
M
Mike Enger
started a topic
3 months ago
For investigators to harmonize their raw mass cytometry data, the DMC recommends using the cytofkit2 application. The cytofkit2 application was developed and deployed by the BDC Seven Bridges team and is designed to analyze mass cytometry data from Flow Cytometry Standard (FCS) files. It includes preprocessing, cell subset detection, cell subset visualization and interpretation, and inference of subset progression.
Inputs: This application requires the user to specify a directory that contains FCS format files for the analysis.
Outputs:
Scatter plot - a PDF format file with a scatter plot of predicted clusters.
Median heatmap - a PDF format file with the heat-map plot that presents the median value of each marker's presence within the clusters.
Mean heatmap - a PDF format file with the heat-map plot presenting the mean value of each marker's presence within the clusters.
RData object - an RDATA format file that contains an R object which can be used for further analysis by the cytofkit2 shiny interactive analysis.
CSV data - a list of CSV format files containing expression-level results for each cluster, mean and median data of markers' presence, as well as information about the percentage of all input file cells in each cluster.
Mike Enger
For investigators to harmonize their raw mass cytometry data, the DMC recommends using the cytofkit2 application. The cytofkit2 application was developed and deployed by the BDC Seven Bridges team and is designed to analyze mass cytometry data from Flow Cytometry Standard (FCS) files. It includes preprocessing, cell subset detection, cell subset visualization and interpretation, and inference of subset progression.
Inputs: This application requires the user to specify a directory that contains FCS format files for the analysis.
Outputs:
Scatter plot - a PDF format file with a scatter plot of predicted clusters.
Median heatmap - a PDF format file with the heat-map plot that presents the median value of each marker's presence within the clusters.
Mean heatmap - a PDF format file with the heat-map plot presenting the mean value of each marker's presence within the clusters.
RData object - an RDATA format file that contains an R object which can be used for further analysis by the cytofkit2 shiny interactive analysis.
CSV data - a list of CSV format files containing expression-level results for each cluster, mean and median data of markers' presence, as well as information about the percentage of all input file cells in each cluster.
Link to Application: https://platform.sb.biodatacatalyst.nhlbi.nih.gov/public/apps/admin/sbg-public-data/cytofkit2-0-99-80