https://github.com/gszep/flowworkspace.jl

Load useful metadata from FlowJo workspace files such as gating strategies and sample groups
https://github.com/gszep/flowworkspace.jl

Last synced: 3 days ago
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Load useful metadata from FlowJo workspace files such as gating strategies and sample groups

• Host: GitHub
• URL: https://github.com/gszep/flowworkspace.jl
• Owner: gszep
• License: mit
• Created: 2021-01-25T12:36:04.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2024-06-08T07:59:15.000Z (11 months ago)
• Last Synced: 2025-03-30T07:16:48.127Z (28 days ago)
• Language: Julia
• Size: 55.6 MB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# FlowWorkspace.jl

This package provides for loading and parsing of [FlowJo Workspace files](https://docs.flowjo.com/flowjo/workspaces-and-samples/ws-savinganalysis) in pure Julia. The gating strategy is parsed as a `DiMetaGraph` and group membership as `Dict`. Together with [GigaSOM.jl](https://github.com/LCSB-BioCore/GigaSOM.jl) this metadata can be used to generate event-level labels for `FCS` datasets.

[![Build Status](https://app.travis-ci.com/gszep/FlowWorkspace.jl.svg?token=UdhYxVPspzofqoNnanY8&branch=master)](https://travis-ci.com/gszep/FlowWorkspace.jl)

[![Coverage](https://codecov.io/gh/gszep/FlowWorkspace.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gszep/FlowWorkspace.jl)

## Installation

Type `] add FlowWorkspace` and then hit ⏎ Return at the REPL. You should see `pkg> add FlowWorkspace`.

## Basic Usage

> :warning: **FCS files under a workspace must have unique names**. This limitation will be removed in future versions

The `load` method returns a tuple of three `DataFrames` and one `Dict`:

* `data` transformed fluorescence values for each event

* `labels` boolean telling us which events have been gated

* `groups` booleans telling us which group each event belongs to

* `gating` Dictionary of graph representations of each gating strategy

```julia

using FlowWorkspace

data,labels,groups,gating = load("workspace.wsp"; files="*.fcs", cols=:setequal)

```