Module Hierarchy

• dimer: root package
  • dimer.archive: utilities and wrappers for working with HDF archives.
  • dimer.archive_tests
  • dimer.config: module that provides configuration file functionality
  • dimer.data: support for dataset IO and manipulation
  • dimer.data_tests
  • dimer.experiment: Created on Jul 11, 2013
  • dimer.filelock
  • dimer.genome: modules for dealing with (mainly importing to datasets) genomic data
    • dimer.genome.bed: Iterator for the BED format ( http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ) Returns chrom, chromStart, chromEnd, name, score
    • dimer.genome.bedops: wrapper to some of the bedops (http://code.google.com/p/bedops/) utilities
    • dimer.genome.bedops_tests
    • dimer.genome.peak: Iterator for the broadPeak and narrowPeak formats (http://genome.ucsc.edu/FAQ/FAQformat.html#format13 and https://genome.ucsc.edu/FAQ/FAQformat.html#format12)
  • dimer.nnet: abstract classes for deep models
    • dimer.nnet.autoencoder: autoencoders
    • dimer.nnet.autoencoder_tests
    • dimer.nnet.base_test_classes: abstract tester methods and common test operations
    • dimer.nnet.config_spec: classes to handle configuration files
    • dimer.nnet.cspec_tests
    • dimer.nnet.monitor
    • dimer.nnet.monitor_tests
    • dimer.nnet.nccn: convolutional neural nets
    • dimer.nnet.nccn_tests
    • dimer.nnet.nnet_tests
    • dimer.nnet.utils: This file contains different utility functions that are not connected in anyway to the networks presented in the tutorials, but rather help in processing the outputs into a more understandable way.
  • dimer.ops: common operations on numpy arrays