Common RNAseq normalization methods
Project description
Python implementation of common RNAseq normalization methods:
CPM (Counts per million)
FPKM (Fragments per kilobase million)
TPM (Transcripts per million)
UQ (Upper quartile)
CUF (Counts adjusted with UQ factors)
TMM (Trimmed mean of M-values)
CTF (Counts adjusted with TMM factors)
Features
Pure Python implementation (no need for R, etc.)
Scikit-learn compatible
Command line interface
Verbose documentation (at least we hope so…)
Tested methods
Install
We recommend installing RNAnorm with pip:
pip install rnanorm
Quick start
Implemented methods can be used from Python or from the command line.
Normalize from Python
Most commonly normalization methods are run from Python. E.g.:
>>> from rnanorm.datasets import load_rnaseq_toy
>>> from rnanorm import FPKM
>>> dataset = load_rnaseq_toy()
>>> dataset.exp
G1 G2 G3 G4 G5
S1 200.0 300.0 500.0 2000.0 7000.0
S2 400.0 600.0 1000.0 4000.0 14000.0
S3 200.0 300.0 500.0 2000.0 17000.0
S4 200.0 300.0 500.0 2000.0 2000.0
>>> fpkm = FPKM(dataset.gtf_path).set_output(transform="pandas")
>>> fpkm.fit_transform(dataset.exp)
G1 G2 G3 G4 G5
S1 100000.0 100000.0 100000.0 200000.0 700000.0
S2 100000.0 100000.0 100000.0 200000.0 700000.0
S3 50000.0 50000.0 50000.0 100000.0 850000.0
S4 200000.0 200000.0 200000.0 400000.0 400000.0
Normalize from command line
Often it is handy to do normalization from the command line:
rnanorm fpkm exp.csv --gtf annotation.gtf --out exp_fpkm.csv
Contribute
To learn about contributing to the code base, read the Contributing section.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file rnanorm-2.0.0rc1.tar.gz.
File metadata
- Download URL: rnanorm-2.0.0rc1.tar.gz
- Upload date:
- Size: 128.7 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.9.17
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | ba055723b145821d7145ec4e0124c34a19708337321a0045a9cf5750fdb6c681 |
|
| MD5 | aadbc42cbbccb162637daa5aa60bcfc5 |
|
| BLAKE2b-256 | dce461046b998307460bc107fe69d9aaf53f06201e5ef3b4c699c2f7f389efcc |
File details
Details for the file rnanorm-2.0.0rc1-py3-none-any.whl.
File metadata
- Download URL: rnanorm-2.0.0rc1-py3-none-any.whl
- Upload date:
- Size: 118.7 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.9.17
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | beb1ce499cbd69f959f2542defa4d542e232f472373c3b6fe14e9da1f69c278e |
|
| MD5 | 1600033b7643ac5fc743087a527682f3 |
|
| BLAKE2b-256 | 63dd917273c1b985643a378f729c7cb5919377cb6fecdb1b44f8b1021c3cfdb3 |
