Index

A

Algorithm (class in blockify.algorithms)

annotate() (in module blockify.annotation), [1] annotate_from_command_line() (in module blockify.annotation), [1]

B

BayesianBlocks (class in blockify.algorithms) blockify module blockify.algorithms module blockify.annotation module, [1] blockify.downsampling module, [1]

blockify.normalization module, [1] blockify.parsers module blockify.segmentation module, [1] blockify.utilities module blocksToDF() (in module blockify.segmentation), [1]

C

compute_ncp_prior() (blockify.algorithms.Algorithm method)

D

downsample() (in module blockify.downsampling), [1]

downsample_from_command_line() (in module blockify.downsampling), [1]

F

file_len() (in module blockify.utilities) finalize() (blockify.segmentation.SegmentationRecord method), [1] fitness() (blockify.algorithms.Algorithm method) (blockify.algorithms.BayesianBlocks method) (blockify.algorithms.OptimalPartitioning method) (blockify.algorithms.PELT method)

G

get_change_points() (blockify.algorithms.OptimalPartitioning static method)

getChromosomesInDF() (in module blockify.utilities) getPeakSummits() (in module blockify.annotation), [1]

I

isSortedBEDFile() (in module blockify.utilities)

isSortedBEDObject() (in module blockify.utilities)

M

module blockify blockify.algorithms blockify.annotation, [1] blockify.downsampling, [1] blockify.normalization, [1] blockify.parsers blockify.segmentation, [1] blockify.utilities

N

normalize() (in module blockify.normalization), [1]

normalize_from_command_line() (in module blockify.normalization), [1]

O

OptimalPartitioning (class in blockify.algorithms)

P

p0_prior() (blockify.algorithms.Algorithm method)

parcelConsecutiveBlocks() (in module blockify.annotation), [1] PELT (class in blockify.algorithms)

S

segment() (blockify.algorithms.Algorithm method) (blockify.algorithms.OptimalPartitioning method) (blockify.algorithms.PELT method) (in module blockify.segmentation), [1]

segment_from_command_line() (in module blockify.segmentation), [1] SegmentationRecord (class in blockify.segmentation), [1] sizeFilter() (in module blockify.annotation), [1]

T

tighten() (in module blockify.annotation), [1]

V

validate_input() (blockify.algorithms.Algorithm static method) validateAnnotationArguments() (in module blockify.annotation), [1]

validateNormalizationArguments() (in module blockify.normalization), [1] validateSegmentationArguments() (in module blockify.segmentation), [1]