Python package wrapping ENCODE epigenomic data for a number of reference cell lines.
Project description
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_datasetTests Coverage
Since some software handling coverages sometimes get slightly different results, here’s three of them:
Preprocessed data for cis-regulatory regions
We have already downloaded and obtained mean and max for each promoter and enhancer region for the cell lines A549, GM12878, H1, HEK293, HepG2, K562, MCF7, taking in consideration all the targets listed in the complete table of epigenomes.
The promoters and enhancers considered are taken from FANTOM, as can be downloaded by using the crr_labels pipeline.
The specific bed files and labels used can be found here for the promoters and here for the enhancers.
Cell line |
Promoters epigenomes |
Enhancers epigenomes |
Features number |
|---|---|---|---|
A549 |
54 |
||
GM12878 |
110 |
||
H1 |
43 |
||
HEK293 |
207 |
||
HepG2 |
209 |
||
K562 |
320 |
||
MCF7 |
101 |
||
All cell lines |
1044 |
Pipeline
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
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