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
- Submodules
- 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
- Submodules
- 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
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 interactionslib5c.algorithms.distributions
- statistical modeling of 5C contact frequencieslib5c.algorithms.filtering
- binning, smoothing, etc.lib5c.algorithms.correlation
- pairwise correlations between replicateslib5c.algorithms.determine_bins
- computing bins to tile 5C regionslib5c.algorithms.donut_filters
- “donut” expected model correctionlib5c.algorithms.enrichment
- computing enrichments for genomic annotations between different 5C interaction classeslib5c.algorithms.expected
- building expected models for 5C datalib5c.algorithms.express
- “Express” normalization algorithmslib5c.algorithms.knight_ruiz
- Knight-Ruiz matrix balancinglib5c.algorithms.outliers
- finding and removing high spatial outliers in 5C contact matriceslib5c.algorithms.qnorm
- quantile normalization standardize distributions between replicateslib5c.algorithms.spline_normalization
- spline-based bias factor normalizationlib5c.algorithms.trimming
- removing “dead” or low-count primers from 5C datasets