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Basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

Regulatory element analysis

basenji_motifs.py

Perform motif analysis on sequences recognized by the first convolution layer filters.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
data_file HDF5 HDF5 file with test_in/test_out keys.

basenji_sat.py

Perform an in silico saturated mutagenesis of the given test sequences.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
input_file HDF5/FASTA HDF5 file with test_in/test_out keys, or FASTA file of sequences.

basenji_map.py

Visualize a sequence's prediction's gradients as a map of influence across the genomic region.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
genes_hdf5_file HDF5 HDF5 file with gene sequences and descriptions.