lib5c package¶
Subpackages¶
- 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
- lib5c.algorithms.clustering package
- 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
- Subpackages
- lib5c.contrib package
- lib5c.core package
- lib5c.operators package
- lib5c.parsers package
- Submodules
- lib5c.parsers.bed module
- lib5c.parsers.bias module
- lib5c.parsers.config module
- lib5c.parsers.counts module
- lib5c.parsers.genes module
- lib5c.parsers.hic module
- lib5c.parsers.loops module
- lib5c.parsers.primer_names module
- lib5c.parsers.primers module
- lib5c.parsers.scaled module
- lib5c.parsers.table module
- lib5c.parsers.util module
- Module contents
- Submodules
- lib5c.plotters package
- Subpackages
- lib5c.plotters.extendable package
- Submodules
- lib5c.plotters.extendable.base_extendable_heatmap module
- lib5c.plotters.extendable.bed_extendable_heatmap module
- lib5c.plotters.extendable.chipseq_extendable_heatmap module
- lib5c.plotters.extendable.cluster_extendable_heatmap module
- lib5c.plotters.extendable.domain_extendable_heatmap module
- lib5c.plotters.extendable.extendable_figure module
- lib5c.plotters.extendable.extendable_heatmap module
- lib5c.plotters.extendable.gene_extendable_heatmap module
- lib5c.plotters.extendable.legend_extendable_heatmap module
- lib5c.plotters.extendable.motif_extendable_heatmap module
- lib5c.plotters.extendable.rectangle_extendable_heatmap module
- lib5c.plotters.extendable.ruler_extendable_heatmap module
- lib5c.plotters.extendable.snp_extendable_heatmap module
- Module contents
- Submodules
- lib5c.plotters.extendable package
- Submodules
- lib5c.plotters.asymmetric_colormap module
- lib5c.plotters.bias_heatmaps module
- lib5c.plotters.boxplots module
- lib5c.plotters.clustering module
- lib5c.plotters.colormaps module
- lib5c.plotters.colorscales module
- lib5c.plotters.convergency module
- lib5c.plotters.correlation module
- lib5c.plotters.curve_fits module
- lib5c.plotters.distance_dependence module
- lib5c.plotters.distribution module
- lib5c.plotters.enrichment module
- lib5c.plotters.expected module
- lib5c.plotters.fits module
- lib5c.plotters.heatmap module
- lib5c.plotters.matrix module
- lib5c.plotters.pca module
- lib5c.plotters.queried_counts_heatmap module
- lib5c.plotters.scatter module
- lib5c.plotters.splines module
- lib5c.plotters.variance module
- Module contents
- Subpackages
- lib5c.structures package
- lib5c.tools package
- Submodules
- lib5c.tools.bias_heatmap module
- lib5c.tools.bin module
- lib5c.tools.boxplot module
- lib5c.tools.colorscale module
- lib5c.tools.convergency module
- lib5c.tools.correlation module
- lib5c.tools.dd_curve module
- lib5c.tools.determine_bins module
- lib5c.tools.distribution module
- lib5c.tools.divide module
- lib5c.tools.enrichment module
- lib5c.tools.expected module
- lib5c.tools.express module
- lib5c.tools.heatmap module
- lib5c.tools.helpers module
- lib5c.tools.hic_extract module
- lib5c.tools.iced module
- lib5c.tools.interaction_score module
- lib5c.tools.kr module
- lib5c.tools.lib5c_toolbox module
- lib5c.tools.log module
- lib5c.tools.outliers module
- lib5c.tools.parents module
- lib5c.tools.pca module
- lib5c.tools.pipeline module
- lib5c.tools.pvalue_histogram module
- lib5c.tools.pvalues module
- lib5c.tools.qnorm module
- lib5c.tools.qvalues module
- lib5c.tools.remove module
- lib5c.tools.smooth module
- lib5c.tools.spline module
- lib5c.tools.subtract module
- lib5c.tools.threshold module
- lib5c.tools.trim module
- lib5c.tools.variance module
- lib5c.tools.visualize_fits module
- lib5c.tools.visualize_splines module
- lib5c.tools.visualize_variance module
- Module contents
- Submodules
- lib5c.util package
- Submodules
- lib5c.util.annotationmap module
- lib5c.util.ast_eval module
- lib5c.util.bed module
- lib5c.util.bedgraph module
- lib5c.util.config module
- lib5c.util.counts module
- lib5c.util.counts_superdict module
- lib5c.util.demo_data module
- lib5c.util.dictionaries module
- lib5c.util.distributions module
- lib5c.util.donut module
- lib5c.util.grouping module
- lib5c.util.lowess module
- lib5c.util.lru_cache module
- lib5c.util.mathematics module
- lib5c.util.metrics module
- lib5c.util.optimization module
- lib5c.util.parallelization module
- lib5c.util.plotting module
- lib5c.util.pretty_decorator module
- lib5c.util.primers module
- lib5c.util.sampling module
- lib5c.util.scales module
- lib5c.util.slicing module
- lib5c.util.sorting module
- lib5c.util.statistics module
- lib5c.util.stratification module
- lib5c.util.system module
- lib5c.util.table module
- Module contents
- Submodules
- lib5c.writers package
Module contents¶
A library for 5C data analysis.
Subpackage structure:
lib5c.algorithms
- main algorithms for analysislib5c.contrib
- integrations with third-party packageslib5c.parsers
- file parsinglib5c.plotters
- data visualizationlib5c.tools
- command line interface forlib5c
lib5c.util
- various utility functionslib5c.writers
- file writing