an interactive explorer for flow cytometry data
Flow Atlas is an interactive data explorer for FCS datasets and their accompanying FlowJo workspace files, such as those coming from the Human Cell Atlas. This tool is built in Julia and allows biologists to interactively inter-operate between FlowJo and modern computational libraries like GigaSOM.jl
To install Flow Atlas, Julia 1.5+ is required. Follow platform specific instructions. In order to make the julia executable available from the command prompt / terminal follow the instructions on adding Julia to the PATH/enviroment; make sure this has been done according to the instructions linked above.
Once julia has been added to the environment, open a command prompt / terminal and type julia. This opens a julis shell; you should see julia>. Then type ] to enter the package manager, and type add FlowAtlas and then hit Return ⏎. You should see pkg> add FlowAtlas.
This installs the most recent version of Flow Atlas and makes it availalbe in your global Julia enviroment. Finally to exit the package manager hit Backspace ⌫; you should see julia> again.
Once inside a julia shell, type ] to enter the package manager and then type update FlowAtlas then hit Return ⏎
⚠️ FCS files under a workspace must have unique names. This limitation will be removed in future versions
Open a julia shell in the directory that contains your workspace and all FCS files (not in sub-folders) and import Flow Altas using using FlowAtlas. The FlowAtlas.run method runs the web application in your default broswer. To launch the web application use the run method
using FlowAtlas
FlowAtlas.run("name_of_my_workspace.wsp")