epigenomic-dataset

Python package wrapping ENCODE epigenomic data for a number of reference cell lines.


License
MIT
Install
pip install epigenomic-dataset==1.2.14

Documentation

epigenomic_dataset

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Python package wrapping ENCODE epigenomic data for several reference cell lines.

How do I install this package?

As usual, just download it using pip:

pip install epigenomic_dataset

Tests Coverage

Since some software handling coverages sometimes get slightly different results, here's three of them:

Coveralls Coverage SonarCloud Coverage Code Climate Coverate

TODO: THE FOLLOWING SECTION WILL NEED RESTRUCTURING IN A LITTLE BIT!

Preprocessed data for cis-regulatory regions

We have already downloaded and obtained the max window value for each promoter and enhancer region for the cell lines A549, GM12878, H1, HEK293, HepG2, K562 and MCF7 in the dataset Fantom and cell lines A549, GM12878, H1, HepG2 and K562 for the Roadmap dataset taking in consideration all the target features listed in the complete table of epigenomes.

The thresholds used for classifying the activations of enhancers and promoters in Fantom are the default explained in the sister pipeline CRR labels which handles the download and preprocessing of the data from Fantom and Roadmap.

Dataset Assembly Window Size Region Cell line Download URL
fantom hg38 256 promoters GM12878 Download
fantom hg38 256 promoters A549 Download
fantom hg38 256 promoters HEK293 Download
fantom hg38 256 promoters HepG2 Download
fantom hg38 256 promoters K562 Download
fantom hg38 256 promoters H1 Download
fantom hg38 256 promoters MCF-7 Download
fantom hg38 256 enhancers GM12878 Download
fantom hg38 256 enhancers A549 Download
fantom hg38 256 enhancers HEK293 Download
fantom hg38 256 enhancers HepG2 Download
fantom hg38 256 enhancers K562 Download
fantom hg38 256 enhancers H1 Download
fantom hg38 256 enhancers MCF-7 Download
fantom hg38 128 promoters GM12878 Download
fantom hg38 128 promoters A549 Download
fantom hg38 128 promoters HEK293 Download
fantom hg38 128 promoters HepG2 Download
fantom hg38 128 promoters K562 Download
fantom hg38 128 promoters H1 Download
fantom hg38 128 promoters MCF-7 Download
fantom hg38 128 enhancers GM12878 Download
fantom hg38 128 enhancers A549 Download
fantom hg38 128 enhancers HEK293 Download
fantom hg38 128 enhancers HepG2 Download
fantom hg38 128 enhancers K562 Download
fantom hg38 128 enhancers H1 Download
fantom hg38 128 enhancers MCF-7 Download
fantom hg38 64 promoters GM12878 Download
fantom hg38 64 promoters A549 Download
fantom hg38 64 promoters HEK293 Download
fantom hg38 64 promoters HepG2 Download
fantom hg38 64 promoters K562 Download
fantom hg38 64 promoters H1 Download
fantom hg38 64 promoters MCF-7 Download
fantom hg38 64 enhancers GM12878 Download
fantom hg38 64 enhancers A549 Download
fantom hg38 64 enhancers HEK293 Download
fantom hg38 64 enhancers HepG2 Download
fantom hg38 64 enhancers K562 Download
fantom hg38 64 enhancers H1 Download
fantom hg38 64 enhancers MCF-7 Download
fantom hg38 1024 promoters GM12878 Download
fantom hg38 1024 promoters A549 Download
fantom hg38 1024 promoters HEK293 Download
fantom hg38 1024 promoters HepG2 Download
fantom hg38 1024 promoters K562 Download
fantom hg38 1024 promoters H1 Download
fantom hg38 1024 promoters MCF-7 Download
fantom hg38 1024 enhancers GM12878 Download
fantom hg38 1024 enhancers A549 Download
fantom hg38 1024 enhancers HEK293 Download
fantom hg38 1024 enhancers HepG2 Download
fantom hg38 1024 enhancers K562 Download
fantom hg38 1024 enhancers H1 Download
fantom hg38 1024 enhancers MCF-7 Download
fantom hg38 512 promoters GM12878 Download
fantom hg38 512 promoters A549 Download
fantom hg38 512 promoters HEK293 Download
fantom hg38 512 promoters HepG2 Download
fantom hg38 512 promoters K562 Download
fantom hg38 512 promoters H1 Download
fantom hg38 512 promoters MCF-7 Download
fantom hg38 512 enhancers GM12878 Download
fantom hg38 512 enhancers A549 Download
fantom hg38 512 enhancers HEK293 Download
fantom hg38 512 enhancers HepG2 Download
fantom hg38 512 enhancers K562 Download
fantom hg38 512 enhancers H1 Download
fantom hg38 512 enhancers MCF-7 Download

Here are the labels for all the considered cell lines.

Dataset Promoters Enhancers
Fantom 200 1000 200 1000
Roadmap 200 1000 200 1000

TODO: align promoters and enhancers in a reference labels dataset.

The complete pipeline used to retrieve the CRR epigenomic data is available here.

Automatic retrieval of preprocessed data

You can automatically retrieve the data as follows:

from epigenomic_dataset import load_epigenomes

X, y = load_epigenomes(
    cell_line = "K562",
    dataset = "fantom",
    region = "promoters",
    window_size = 256,
    root = "datasets" # Path where to download data
)

Pipeline for epigenomic data

The considered raw data are from this query from the ENCODE project

You can find the complete table of the available epigenomes here. These datasets were selected to have (at time of the writing, 07/02/2020) the least possible amount of known problems, such as low read resolution.

You can run the pipeline as follows: suppose you want to extract the epigenomic features for the cell lines HepG2 and H1:

from epigenomic_dataset import build

build(
    bed_path="path/to/my/bed/file.bed",
    cell_lines=["HepG2", "H1"]
)

If you want to specify where to store the files use:

from epigenomic_dataset import build

build(
    bed_path="path/to/my/bed/file.bed",
    cell_lines=["HepG2", "H1"],
    path="path/to/my/target"
)

By default, the downloaded bigWig files are not deleted. You can choose to delete the files as follows:

from epigenomic_dataset import build

build(
    bed_path="path/to/my/bed/file.bed",
    cell_lines=["HepG2", "H1"],
    path="path/to/my/target",
    clear_download=True
)