Module `epiclass.utils`

Sub-modules

epiclass.utils.analyze_hdf5_vals: Make violing plots of the statistics of a set of hdf5 samples.
epiclass.utils.analyze_metadata: Analyze metadata content.
epiclass.utils.augment_predict_file: Augment a label prediction file with new metadata categories …
epiclass.utils.bed_utils: This module provides a collection of utilities for manipulating and analyzing genomic data. The utilities are useful for performing operations such as …
epiclass.utils.bg_val_transfer: Transfer bedgraph values to new positions based on a reference bed file.
epiclass.utils.bigwig_metrics: This module provides functionalities compute a metric on given regions from bigwig files. Uses pyBigWig.
epiclass.utils.check_dir: Utility script to check a directory and create it if needed …
epiclass.utils.chrY_bigwig_mean: This module provides functionalities compute the chrY and chrX mean signal from bigwig files.
epiclass.utils.classification_merging_utils: Utility functions for merging classification results.
epiclass.utils.clean_hdf5: Module: clean_hdf5 …
epiclass.utils.collect_hdf5_vals: Collect values from hdf5 files and save them as csv and/or hdf5.
epiclass.utils.compute_bin_metrics: This module provides a command-line interface for computing the metric of signal bins for a given set of genomic data …
epiclass.utils.compute_pca: Compute PCA for some hardcoded datasets. (dataset selection done in .sh script)
epiclass.utils.compute_umap: Compute various UMAP embeddings (modify nearest neighboors + densMap or not) for some hardcoded datasets.
epiclass.utils.create_confusion_matrices: This Python script is intended to merge or create confusion matrices. It uses the epiclass library's ConfusionMatrixWriter for tasks related to …
epiclass.utils.epirr_corr: Create a correlation matrix based on the correlation of the signals of all datasets for a given epiRR (concatenated signals)
epiclass.utils.extract_metrics: Extract metrics for other classifiers output files, or csv output of cometML for neural networks.
epiclass.utils.extract_output_info: Extract specific information from what epiML prints …
epiclass.utils.general_utility: For lost little functions that don't fit anywhere else.
epiclass.utils.hdf5_to_float32: This module provides functionalities to copy HDF5 files to a new directory, convert their datasets to float32 data type, and repack them to reduce …
epiclass.utils.merge_all_predictions: Merge predictions files produced from epilap program. Tightly linked with the output of augment_predict_file.py.
epiclass.utils.merge_validation_predictions: Merge validation prediction files from splitX folders.
epiclass.utils.metadata_utils: Metadata analysis basic utility functions. Also defines some constants.
epiclass.utils.modify_metadata: Functions to perform more complex operations on the metadata.
epiclass.utils.my_logging: Implement logging of specific data through comet logger.
epiclass.utils.notebooks
epiclass.utils.preconditions: Check for specific conditions before running the main program, .e.g git in clean state, metadata passes all test flags, etc …
epiclass.utils.shap
epiclass.utils.ssh_utils: Utility functions for SSH and SCP.
epiclass.utils.time: Time utilities
epiclass.utils.winsorize_hdf5: Module: winsorize_hdf5 …
epiclass.utils.write_chrom_filter: Create a custom bed filter for each chromosome, to select a fixed region on the second arm center.