lib5c.algorithms package

Subpackages

• lib5c.algorithms.clustering package
  • Submodules
    • lib5c.algorithms.clustering.adjacency module
    • lib5c.algorithms.clustering.enclave module
    • lib5c.algorithms.clustering.greedy module
    • lib5c.algorithms.clustering.knn module
    • lib5c.algorithms.clustering.quasicontiguity module
    • lib5c.algorithms.clustering.util module
    • lib5c.algorithms.clustering.valley module
  • Module contents
• lib5c.algorithms.filtering package
  • Submodules
    • lib5c.algorithms.filtering.bin_bin_filtering module
    • lib5c.algorithms.filtering.filter_functions module
    • lib5c.algorithms.filtering.fragment_bin_filtering module
    • lib5c.algorithms.filtering.fragment_fragment_filtering module
    • lib5c.algorithms.filtering.unsmoothable_columns module
    • lib5c.algorithms.filtering.util module
  • Module contents
• lib5c.algorithms.variance package
  • Submodules
    • lib5c.algorithms.variance.combined module
    • lib5c.algorithms.variance.cross_rep module
    • lib5c.algorithms.variance.deviation module
    • lib5c.algorithms.variance.estimate_variance module
    • lib5c.algorithms.variance.local module
    • lib5c.algorithms.variance.lognorm_dispersion module
    • lib5c.algorithms.variance.mle module
    • lib5c.algorithms.variance.nbinom_dispersion module
  • Module contents

Submodules

• lib5c.algorithms.convergency module
• lib5c.algorithms.correlation module
• lib5c.algorithms.determine_bins module
• lib5c.algorithms.donut_filters module
• lib5c.algorithms.enrichment module
• lib5c.algorithms.expected module
• lib5c.algorithms.express module
• lib5c.algorithms.knight_ruiz module
• lib5c.algorithms.outliers module
• lib5c.algorithms.pca module
• lib5c.algorithms.qnorm module
• lib5c.algorithms.spline_normalization module
• lib5c.algorithms.thresholding module
• lib5c.algorithms.trimming module

Module contents

Subpackage containing algorithms for 5C data analysis.

Subpackage structure:

• lib5c.algorithms.clustering - algorithms for clustering together 5C interactions

• lib5c.algorithms.distributions - statistical modeling of 5C contact frequencies

• lib5c.algorithms.filtering - binning, smoothing, etc.

• lib5c.algorithms.correlation - pairwise correlations between replicates

• lib5c.algorithms.determine_bins - computing bins to tile 5C regions

• lib5c.algorithms.donut_filters - “donut” expected model correction

• lib5c.algorithms.enrichment - computing enrichments for genomic annotations between different 5C interaction classes

• lib5c.algorithms.expected - building expected models for 5C data

• lib5c.algorithms.express - “Express” normalization algorithms

• lib5c.algorithms.knight_ruiz - Knight-Ruiz matrix balancing

• lib5c.algorithms.outliers - finding and removing high spatial outliers in 5C contact matrices

• lib5c.algorithms.qnorm - quantile normalization standardize distributions between replicates

• lib5c.algorithms.spline_normalization - spline-based bias factor normalization

• lib5c.algorithms.trimming - removing “dead” or low-count primers from 5C datasets