tiangzlab/omicsclaw/bulkrna-splicing

bulkrna-splicing

When to use

Summarize existing splicing tests; this skill does not call rMATS or SUPPA2. See the description for adjacent skills.

Use from a step

from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("bulkrna-splicing")
# Supply DataFrames read with read_input(..., reader=...) for your CSV layout.
result = library.summarize(events)
write_output(result, "tables/result.csv")

The synthetic worked step is in examples/example_step.py.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->

summarize(events, *, dpsi_cutoff=0.1, padj_cutoff=0.05)

Summarize upstream event tests without changing the table.

:param events: DataFrame with gene, event_type, delta_psi and padj columns. :param dpsi_cutoff: CLI default 0.1; absolute delta-PSI must exceed it. :param padj_cutoff: CLI default 0.05; adjusted p values must be below it. :returns: Copy of events with diagnostics in attrs. :raises ValueError: Required columns, probabilities or thresholds are invalid.

run_info(result, *, keep=True)

Read event counts and threshold diagnostics.

:param result: DataFrame returned by summarize. :param keep: Default True; False removes diagnostic attrs. :returns: Diagnostic dictionary, empty after removal.

significant_events(result)

Return events passing both strict thresholds.

:param result: DataFrame returned by summarize, with diagnostics retained. :returns: New filtered DataFrame. :raises KeyError: Diagnostics are absent.

volcano_figure(result)

Plot delta-PSI against upstream adjusted significance.

:param result: Event table with delta_psi and padj. :returns: A matplotlib Figure, without writing files. :raises KeyError: Required columns are absent.

<!-- api:end -->

Methods and parameters

See parameters and methodology.

Gotchas

• summarize uses strict abs(delta_psi) > dpsi_cutoff and padj < padj_cutoff.
• Rename upstream columns to gene, event_type, delta_psi, padj; summarize rejects missing fields.
• significant_events filters supplied p values; it does not estimate significance.

Inputs and outputs

The library returns objects without file writes. CLI inventory:

Inputs

• File types: .csv

Outputs

• tables/significant_events.csv
• tables/splicing_events.csv
• figures/dpsi_distribution.png
• figures/event_type_distribution.png
• figures/volcano_splicing.png
• report.md
• result.json

CLI

python skills/bulkrna/bulkrna-splicing/bulkrna_splicing.py --demo --output /tmp/bulkrna-splicing

See also

• Output contract

Dependencies

matplotlib, numpy, pandas, scipy