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Launch iSEE Copy Specifications

Process Details

  • Name: launch_isee_copy
  • Process UUID: 5Lbdb82d8fMzhSH2SWVnmlhjsRyA3U
  • Process Group: SingleCell

Overview

This process launches the interactive SummarizedExperiment Explorer (iSEE) browser from a SingleCellExperiment object stored in an RDS file. iSEE provides an interactive web-based interface for exploring single-cell RNA sequencing data, allowing users to create customizable plots, tables, and visualizations to investigate their datasets through a user-friendly graphical interface.

This process is implemented in Perl, which generates and executes an R script for launching the iSEE application.

Key Functionality

  • Interactive Data Exploration: Launches a web-based iSEE browser for interactive exploration of single-cell data
  • Shiny Application Hosting: Sets up a Shiny server on port 8789 accessible from any network interface
  • SingleCellExperiment Integration: Directly loads and visualizes data from SingleCellExperiment objects stored in RDS format

Input/Output Specification

Inputs

Required Inputs

  • RDS File
    • Description: A SingleCellExperiment object saved in RDS format containing single-cell RNA sequencing data
    • Format: RDS

Outputs

  • Output File
    • Description: Process execution output and log information
    • Format: out

References & Resources

  • Tool Documentation: Contact the team for details on launch_iSEE.R
  • Related Papers: Rue-Albrecht, K., Marini, F., Soneson, C., & Lun, A. T. (2018). iSEE: Interactive SummarizedExperiment Explorer. F1000Research, 7, 741. https://doi.org/10.12688/f1000research.14966.1