Flowkit

What it does

When your agent uses it

• Reproducible gate counts
• Population percentages
• Gated fluorescence summaries
• Reproducing a FlowJo analysis in Python

Example prompts

• “Use the flowkit skill to analyz flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms…”
• “/flowkit”

Requirements

• Python 3
• Compatibility (from SKILL.md): Requires Python 3.13 with flowkit==1.3.2 for the tested environment. Dependencies include FlowIO, FlowUtils, NumPy, pandas, SciPy, lxml, and Bokeh. Installation needs network access; analysis uses local FCS/XML/WSP files without credentials. FlowUtils needs a C compiler if a compatible wheel is unavailable.

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Identify the analysis definition. Use Session for a programmatic or
2. 2Inspect samples and channel identities. Match detector/PnN labels to
3. 3Establish the coordinate system. Determine whether the supplied events
4. 4Check the hierarchy. Preserve parent gates and full gate paths, including
5. 5Analyze and inspect. Run on all events, then check gate overlays and
6. 6Export counts with denominators and provenance. Keep gate paths,

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 1 file in scripts/ (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • uv
  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • flowkit.readthedocs.io
  • github.com
  • doi.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires Python 3.13 with flowkit==1.3.2 for the tested environment. Dependencies include FlowIO, FlowUtils, NumPy, pandas, SciPy, lxml, and Bokeh. Installation needs network access; analysis uses local FCS/XML/WSP files without credentials. FlowUtils needs a C compiler if a compatible wheel is unavailable.

  From compatibility in the SKILL.md frontmatter.

Context cost

Flowkit loads about 2.2k tokens when it runs, and up to ~5k if it reads all its reference files. Until then it costs about 100 tokens; SKILL.md has 763 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~100

When it runs · the whole SKILL.md, loaded when a task matches

~2.2k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 763 words, ~2,187 tokens.

name

flowkit

description

Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces. Use for reproducible gate counts, population percentages, gated fluorescence summaries, or reproducing a FlowJo analysis in Python. For FCS metadata inspection or file-format repair alone, use FlowIO.

compatibility

Requires Python 3.13 with flowkit==1.3.2 for the tested environment. Dependencies include FlowIO, FlowUtils, NumPy, pandas, SciPy, lxml, and Bokeh. Installation needs network access; analysis uses local FCS/XML/WSP files without credentials. FlowUtils needs a C compiler if a compatible wheel is unavailable.

license

MIT

metadata.version

1.1

metadata.skill-author

K-Dense Inc.

metadata.last-reviewed

2026-09-30

uv venv --python 3.13 .venv-flowkit
uv pip install --python .venv-flowkit/bin/python "flowkit==1.3.2"
.venv-flowkit/bin/python -c "import flowkit; print(flowkit.__version__)"

FLOWKIT_SKILL_DIR="skills/flowkit"
uv run --no-project --python 3.13 --with "flowkit==1.3.2" \
  python "$FLOWKIT_SKILL_DIR/scripts/analyze_gates.py" \
  --gatingml gates.xml --fcs sample.fcs --output-dir results-gatingml

uv run --no-project --python 3.13 --with "flowkit==1.3.2" \
  python "$FLOWKIT_SKILL_DIR/scripts/analyze_gates.py" \
  --workspace study.wsp --group "Study" \
  --fcs sample-a.fcs sample-b.fcs --output-dir results-workspace

import flowkit as fk
import numpy as np

sample = fk.Sample("sample.fcs")
strategy = fk.GatingStrategy()
strategy.add_comp_matrix(
    "spill", fk.Matrix(
        np.array([[1.0, 0.1], [0.2, 1.0]]), ["FL1-A", "FL2-A"],
        fluorochromes=["FITC", "PE"],
    )
)
logicle = fk.transforms.LogicleTransform(
    param_t=262144, param_w=0.5, param_m=4.5, param_a=0
)
strategy.add_transform("logicle", logicle)
strategy.add_gate(
    fk.gates.RectangleGate("Cells", [
        fk.Dimension("FSC-A", range_min=50, range_max=300)
    ]),
    gate_path=("root",),
)
thresholds = logicle.apply(np.array([50.0, 600.0]))
strategy.add_gate(
    fk.gates.RectangleGate("Positive", [
        fk.Dimension(
            "FL1-A", compensation_ref="spill", transformation_ref="logicle",
            range_min=float(thresholds[0]), range_max=float(thresholds[1]),
        )
    ]),
    gate_path=("root", "Cells"),
)
session = fk.Session(gating_strategy=strategy, fcs_samples=[sample])
session.analyze_samples(use_mp=False)
report = session.get_analysis_report()
print(report[["sample_id", "gate_path", "gate_name", "count",
              "absolute_percent", "relative_percent"]])
with open("gates.xml", "xb") as handle:
    session.export_gml(handle)

© K-Dense-AI, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts, references) in skills/flowkit of K-Dense-AI/scientific-agent-skills.

• SKILL.md
• references/compensation-and-gating.md
• references/workspaces-and-results.md
• scripts/analyze_gates.py

Open the folder on GitHubat commit 92ace75

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

• lingxling/awesome-skills-cnclaude-scientific-skills/skills/flowkit