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flowio

by K-Dense-AI

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Installation

Pick a client and clone the repository into its skills directory.

Installation

Quick info

Author
K-Dense-AI
Category
Security
GitHub repo

About this skill

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

How to use

  1. Zainstaluj bibliotekę FlowIO za pomocą polecenia uv pip install flowio (wymagany Python 3.9 lub nowszy). 2. Zaimportuj moduł FlowData: from flowio import FlowData i wczytaj plik FCS poleceniem flow_data = FlowData('experiment.fcs'). 3. Sprawdź podstawowe informacje o pliku — wersję FCS, liczbę zdarzeń i etykiety kanałów za pomocą atrybutów flow_data.version, flow_data.event_count i flow_data.pnn_labels. 4. Ekstrahuj dane zdarzeń jako tablicę NumPy (wymiary: liczba zdarzeń × kanały) poleceniem events = flow_data.as_array(). 5. Aby utworzyć nowy plik FCS, przygotuj dane w postaci tablicy NumPy i listę nazw kanałów, następnie użyj funkcji create_fcs('output.fcs', data, channels) z modułu flowio. 6. Wykorzystaj wyekstrahowane dane do dalszych operacji — konwersji do DataFrame, eksportu do CSV lub przekazania do narzędzi analizy zaawansowanej takich jak FlowKit.

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