rnanorm

library2.2.0pypypi✓ verified 82d ago

Rnanorm provides common RNA-seq normalization methods (TPM, CPM, FPKM, TMM, etc.) with a scikit-learn-like API. Current version 2.2.0 requires Python >=3.9, <3.14. The library is actively maintained with regular releases.

ai-ml data

pip install rnanorm

github ↗package ↗

INSTALL

IMPORT

SIG · RNANORM

rnanorm

ai-mlpythonv2.2.0

Install

16.7s avg

Import

—

Disk

369MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.2.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 16.7s · import 0.000s · 357MB

369MB installed

● package 369MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

CPM

✓ from rnanorm import CPM

✗ from rnanorm.datasets import CountData

TMM

✓ from rnanorm import TMM

TPM

✓ from rnanorm import TPM

Basic usage: load example count data, apply TPM normalization with dummy gene lengths.

import pandas as pd from rnanorm import TPM from rnanorm.datasets import CountData # Load example dataset counts = CountData() exp = counts.expression # TPM normalization (requires gene lengths) # For demo, use dummy lengths (1 for all genes) lengths = pd.Series(1.0, index=exp.columns) tpm = TPM().set_output(transform='pandas').fit_transform(exp, lengths) print(tpm.iloc[:5, :5])

Debug

Known issues

breakingIn version 2.0.0, the API changed from fit/transform on raw counts to requiring explicit gene lengths for length-dependent methods (TPM, FPKM). The 'expression' attribute of CountData now returns a DataFrame, not an object with .counts.

fix

Upgrade code to pass lengths to fit_transform. See migration guide: https://rnanorm.readthedocs.io/en/latest/migration.html

affects: <2.0.0

breakingCountData is no longer importable directly from rnanorm; it must be imported from rnanorm.datasets.

fix

Change 'from rnanorm import CountData' to 'from rnanorm.datasets import CountData'

affects: >=2.0.0

gotchaLength-dependent methods (TPM, FPKM) require gene lengths as a pandas Series or array with the same index as the expression DataFrame columns. Using wrong or missing lengths will silently produce incorrect results.

fix

Always provide correct gene lengths; verify by checking that the sum of each sample's TPM is approximately 1e6.

affects: >=2.0.0

gotchaThe set_output(transform='pandas') method must be called before fit_transform to get a DataFrame output; otherwise output is a numpy array.

fix

Chain .set_output(transform='pandas') on the estimator before calling fit_transform.

affects: >=2.0.0

deprecatedThe 'log1p' parameter in some normalizers is deprecated and will be removed in future versions.

fix

Apply log transformation manually after normalization using numpy.log1p.

affects: >=2.0.0

Upgrade

Version history

2.2.0latest on PyPI · released Jan 29, 2025

Audit

Dependencies

scikit-learnrequiredAPI design and base classes

pandasrequiredData handling

numpyrequiredArray operations

Agent activity

11 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/genialis/RNAnorm ↗

packagehttps://pypi.org/project/rnanorm/ ↗