Package: epigenomic-dataset
Python package wrapping ENCODE epigenomic data
for several reference cell lines.How do I install this package?As usual, just download it using pip:pipinstallepigenomic_datasetTests CoverageSince some software handling coverages sometimes get slightly
different results, here’s three of them:TODO: THE FOLLOWING SECTION WILL NEED RESTRUCTURING IN A LITTLE BIT!Preprocessed data for cis-regulatory regionsWe 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 listedin 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 pipelineCRR labelswhich handles the download and preprocessing of the data from Fantom and Roadmap.DatasetAssemblyWindow SizeRegionCell lineDownload URLfantomhg38256promotersGM12878Downloadfantomhg38256promotersA549Downloadfantomhg38256promotersHEK293Downloadfantomhg38256promotersHepG2Downloadfantomhg38256promotersK562Downloadfantomhg38256promotersH1Downloadfantomhg38256promotersMCF-7Downloadfantomhg38256enhancersGM12878Downloadfantomhg38256enhancersA549Downloadfantomhg38256enhancersHEK293Downloadfantomhg38256enhancersHepG2Downloadfantomhg38256enhancersK562Downloadfantomhg38256enhancersH1Downloadfantomhg38256enhancersMCF-7Downloadfantomhg38128promotersGM12878Downloadfantomhg38128promotersA549Downloadfantomhg38128promotersHEK293Downloadfantomhg38128promotersHepG2Downloadfantomhg38128promotersK562Downloadfantomhg38128promotersH1Downloadfantomhg38128promotersMCF-7Downloadfantomhg38128enhancersGM12878Downloadfantomhg38128enhancersA549Downloadfantomhg38128enhancersHEK293Downloadfantomhg38128enhancersHepG2Downloadfantomhg38128enhancersK562Downloadfantomhg38128enhancersH1Downloadfantomhg38128enhancersMCF-7Downloadfantomhg3864promotersGM12878Downloadfantomhg3864promotersA549Downloadfantomhg3864promotersHEK293Downloadfantomhg3864promotersHepG2Downloadfantomhg3864promotersK562Downloadfantomhg3864promotersH1Downloadfantomhg3864promotersMCF-7Downloadfantomhg3864enhancersGM12878Downloadfantomhg3864enhancersA549Downloadfantomhg3864enhancersHEK293Downloadfantomhg3864enhancersHepG2Downloadfantomhg3864enhancersK562Downloadfantomhg3864enhancersH1Downloadfantomhg3864enhancersMCF-7Downloadfantomhg381024promotersGM12878Downloadfantomhg381024promotersA549Downloadfantomhg381024promotersHEK293Downloadfantomhg381024promotersHepG2Downloadfantomhg381024promotersK562Downloadfantomhg381024promotersH1Downloadfantomhg381024promotersMCF-7Downloadfantomhg381024enhancersGM12878Downloadfantomhg381024enhancersA549Downloadfantomhg381024enhancersHEK293Downloadfantomhg381024enhancersHepG2Downloadfantomhg381024enhancersK562Downloadfantomhg381024enhancersH1Downloadfantomhg381024enhancersMCF-7Downloadfantomhg38512promotersGM12878Downloadfantomhg38512promotersA549Downloadfantomhg38512promotersHEK293Downloadfantomhg38512promotersHepG2Downloadfantomhg38512promotersK562Downloadfantomhg38512promotersH1Downloadfantomhg38512promotersMCF-7Downloadfantomhg38512enhancersGM12878Downloadfantomhg38512enhancersA549Downloadfantomhg38512enhancersHEK293Downloadfantomhg38512enhancersHepG2Downloadfantomhg38512enhancersK562Downloadfantomhg38512enhancersH1Downloadfantomhg38512enhancersMCF-7DownloadHere are the labels for all the considered cell lines.DatasetPromotersEnhancersFantom20010002001000Roadmap20010002001000TODO: align promoters and enhancers in a reference labels dataset.The complete pipeline used to retrieve the CRR epigenomic data is availablehere.Automatic retrieval of preprocessed dataYou can automatically retrieve the data as follows:fromepigenomic_datasetimportload_epigenomesX,y=load_epigenomes(cell_line="K562",dataset="fantom",region="promoters",window_size=256,root="datasets"# Path where to download data)Pipeline for epigenomic dataThe considered raw data are fromthis query from the ENCODE projectYou can find thecomplete 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:fromepigenomic_datasetimportbuildbuild(bed_path="path/to/my/bed/file.bed",cell_lines=["HepG2","H1"])If you want to specify where to store the files use:fromepigenomic_datasetimportbuildbuild(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:fromepigenomic_datasetimportbuildbuild(bed_path="path/to/my/bed/file.bed",cell_lines=["HepG2","H1"],path="path/to/my/target",clear_download=True)