Index

_

__delattr__ (imfusion.util.tabix.GtfFile attribute) __format__() (imfusion.util.tabix.GtfFile method) __getattribute__ (imfusion.util.tabix.GtfFile attribute) __hash__ (imfusion.util.tabix.GtfFile attribute) __reduce__() (imfusion.util.tabix.GtfFile method)

__reduce_ex__() (imfusion.util.tabix.GtfFile method) __setattr__ (imfusion.util.tabix.GtfFile attribute) __sizeof__() (imfusion.util.tabix.GtfFile method) __str__ (imfusion.util.tabix.GtfFile attribute)

A

anchor_genome (Fusion attribute) (Insertion attribute) anchor_transposon (Fusion attribute) (Insertion attribute)

annotate_fusions() (in module imfusion.util.fusions)

B

blacklist_for_genes() (in module imfusion.util.reference) blacklist_for_regions() (in module imfusion.util.reference)

build_reference() (in module imfusion.aligners.tophat2)

C

check_features() (in module imfusion.util.check) compress() (imfusion.util.tabix.GtfFile class method)

concatenate_fastas() (in module imfusion.util.reference)

D

de_exon() (in module imfusion.expression.de_test) de_exon_single() (in module imfusion.expression.de_test) DeExonResult (class in imfusion.expression.de_test)

DeExonSingleResult (class in imfusion.expression.de_test) direction (DeExonResult attribute) (DeExonSingleResult attribute)

E

exon_counts() (in module imfusion.expression.counts)

exon_split (DeExonResult attribute) (DeExonSingleResult attribute)

F

feature_counts() (in module imfusion.expression.counts) feature_name (Fusion attribute) (Insertion attribute) feature_strand (Fusion attribute) (Insertion attribute) feature_type (Fusion attribute) fetch() (imfusion.util.tabix.GtfFile method) filter_blacklist() (in module imfusion.util.insertions)

filter_invalid_insertions() (in module imfusion.util.insertions) filter_unexpected_sites() (in module imfusion.util.insertions) filter_wrong_orientation() (in module imfusion.util.insertions) flank_genome (Fusion attribute) (Insertion attribute) flank_transposon (Fusion attribute) (Insertion attribute) Fusion (class in imfusion.model)

G

gene_id (Fusion attribute) (Insertion attribute) gene_name (Fusion attribute) (Insertion attribute) gene_strand (Fusion attribute) (Insertion attribute) get_bowtie_version() (in module imfusion.aligners.tophat2)

get_gene() (imfusion.util.tabix.GtfFile method) get_region() (imfusion.util.tabix.GtfFile method) get_version() (in module imfusion.aligners.tophat2) GtfFile (class in imfusion.util.tabix)

I

id (Insertion attribute) identify_insertions() (in module imfusion.aligners.tophat2)

Insertion (class in imfusion.model)

M

mask_regions() (in module imfusion.util.reference)

merge_samples() (in module imfusion.merge)

N

nb_fit (DeExonSingleResult attribute)

O

orientation (Insertion attribute)

P

p_value (DeExonResult attribute) (DeExonSingleResult attribute) place_fusions() (in module imfusion.util.fusions) plot_boxplot() (imfusion.expression.de_test.DeExonResult method)

plot_fit() (imfusion.expression.de_test.DeExonSingleResult method) plot_sums() (imfusion.expression.de_test.DeExonResult method) (imfusion.expression.de_test.DeExonSingleResult method) position (Insertion attribute)

S

sample_id (Insertion attribute) sample_split (DeExonResult attribute) (DeExonSingleResult attribute) seqname (Fusion attribute) (Insertion attribute) sort() (imfusion.util.tabix.GtfFile class method) spanning_mates (Insertion attribute) spanning_reads (Fusion attribute) (Insertion attribute)

strand (Insertion attribute) strand_genome (Fusion attribute) strand_transposon (Fusion attribute) sums (DeExonResult attribute) (DeExonSingleResult attribute) supporting_mates (Fusion attribute) (Insertion attribute) supporting_spanning_mates (Fusion attribute)

T

test_ctgs() (in module imfusion.ctg)

test_de() (in module imfusion.ctg)