Index

A

add() (emase.Sparse3DMatrix.Sparse3DMatrix method) add_value() (emase.Sparse3DMatrix.Sparse3DMatrix method) AlignmentMatrixFactory (class in emase.AlignmentMatrixFactory)

AlignmentPropertyMatrix (class in emase.AlignmentPropertyMatrix) Axis (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix attribute)

B

bundle() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

C

cleanup() (emase.AlignmentMatrixFactory.AlignmentMatrixFactory method) combine() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) (emase.Sparse3DMatrix.Sparse3DMatrix method) copy() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) (emase.Sparse3DMatrix.Sparse3DMatrix method)

count_alignments() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) count_unique_reads() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

E

emase.__init__ (module) emase.AlignmentMatrixFactory (module) emase.AlignmentPropertyMatrix (module) emase.EMfactory (module)

emase.Sparse3DMatrix (module) EMfactory (class in emase.EMfactory) enum() (in module emase.AlignmentPropertyMatrix) export_posterior_probability() (emase.EMfactory.EMfactory method)

F

finalize() (emase.Sparse3DMatrix.Sparse3DMatrix method)

G

get_allelic_expression() (emase.EMfactory.EMfactory method) get_cross_section() (emase.Sparse3DMatrix.Sparse3DMatrix method) get_read_data() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

get_reads_aligned_to_locus() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) get_unique_reads() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

L

load_groups() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

M

multiply() (emase.Sparse3DMatrix.Sparse3DMatrix method)

N

normalize_reads() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

P

prepare() (emase.AlignmentMatrixFactory.AlignmentMatrixFactory method) (emase.EMfactory.EMfactory method) print_read() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

produce() (emase.AlignmentMatrixFactory.AlignmentMatrixFactory method) pull_alignments_from() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method)

R

report_alignment_counts() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) report_depths() (emase.EMfactory.EMfactory method) report_read_counts() (emase.EMfactory.EMfactory method)

reset() (emase.EMfactory.EMfactory method) (emase.Sparse3DMatrix.Sparse3DMatrix method) run() (emase.EMfactory.EMfactory method)

S

save() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) (emase.Sparse3DMatrix.Sparse3DMatrix method) set_value() (emase.Sparse3DMatrix.Sparse3DMatrix method)

Sparse3DMatrix (class in emase.Sparse3DMatrix) sum() (emase.AlignmentPropertyMatrix.AlignmentPropertyMatrix method) (emase.Sparse3DMatrix.Sparse3DMatrix method)

U

update_allelic_expression() (emase.EMfactory.EMfactory method)

update_probability_at_read_level() (emase.EMfactory.EMfactory method)