API document
Prediction of transcription factor binding
This uses the example data described here.
from ananse.peakpredictor import predict_peaks
import glob
outdir = "heart.binding"
histone_files = glob.glob("ANANSE_example_data/atac/heart*bam")
atac_files = glob.glob("ANANSE_example_data/H3K27ac/heart*bam")
reference = "ANANSE.REMAP.model.v1.0/"
def binding(args):
predict_peaks(
outdir,
atac_bams=atac_files,
histone_bams=histone_files,
reference=reference,
genome="hg38",
)
Working with Network
Class
The Network
class include all functions used to infer cell type specific gene regulatory network.
import glob
from ananse.network import Network
from dask.distributed import Client
b = Network(
genome="hg38",
include_promoter=True,
include_enhancer=True
)
# Simple default dask
with Client() as client:
b.run_network(
binding="heart.binding/binding.h5",
fin_expression=glob.glob("heart.binding/heart*TPM.txt"),
outfile="heart.network.txt",
)