Index

A

after (DeResult attribute) (DeSingleResult attribute)

Aligner (class in imfusion.insertions.aligners)

B

base_path (imfusion.build.indexers.Reference attribute) before (DeResult attribute) (DeSingleResult attribute)

build() (imfusion.build.indexers.Indexer method)

C

check_dependencies() (imfusion.build.indexers.Indexer method) (imfusion.insertions.aligners.Aligner method) configure_args() (imfusion.build.indexers.Indexer class method) (imfusion.build.indexers.StarIndexer class method) (imfusion.insertions.aligners.Aligner class method) (imfusion.insertions.aligners.StarAligner class method)

counts (DeGeneResult attribute)

D

DeGeneResult (class in imfusion.expression.test) dependencies (imfusion.build.indexers.Indexer attribute) (imfusion.build.indexers.StarIndexer attribute) (imfusion.build.indexers.TophatIndexer attribute) (imfusion.insertions.aligners.Aligner attribute) (imfusion.insertions.aligners.StarAligner attribute)

DeResult (class in imfusion.expression.test) DeSingleResult (class in imfusion.expression.test) direction (DeGeneResult attribute) (DeResult attribute) (DeSingleResult attribute) dropped_samples (DeResult attribute)

E

estimate_size_factors() (in module imfusion.expression)

exon_gtf_path (imfusion.build.indexers.Reference attribute)

F

fasta_path (imfusion.build.indexers.Reference attribute) features_path (imfusion.build.indexers.Reference attribute)

from_args() (imfusion.build.indexers.Indexer class method) (imfusion.insertions.aligners.Aligner class method)

G

generate_exon_counts() (in module imfusion.expression)

gtf_path (imfusion.build.indexers.Reference attribute)

I

identify_insertions() (imfusion.insertions.aligners.Aligner method) (imfusion.insertions.aligners.StarAligner method) (imfusion.insertions.aligners.TophatAligner method)

index_path (imfusion.build.indexers.Reference attribute) (imfusion.build.indexers.TophatReference attribute) indexed_gtf_path (imfusion.build.indexers.Reference attribute) Indexer (class in imfusion.build.indexers)

N

negative_samples (DeGeneResult attribute) (DeResult attribute) (DeSingleResult attribute)

normalize_counts() (in module imfusion.expression)

P

p_value (DeGeneResult attribute) (DeResult attribute) (DeSingleResult attribute) plot_boxplot() (imfusion.expression.test.DeGeneResult method) (imfusion.expression.test.DeResult method)

plot_sums() (imfusion.expression.test.DeResult method) (imfusion.expression.test.DeSingleResult method) positive_sample (DeSingleResult attribute) positive_samples (DeGeneResult attribute) (DeResult attribute)

R

read_exon_counts() (in module imfusion.expression)

Reference (class in imfusion.build.indexers)

S

StarAligner (class in imfusion.insertions.aligners)

StarIndexer (class in imfusion.build.indexers) StarReference (class in imfusion.build.indexers)

T

test_de() (in module imfusion.expression) test_de_exon() (in module imfusion.expression) test_de_exon_single() (in module imfusion.expression) test_de_gene() (in module imfusion.expression) TophatAligner (class in imfusion.insertions.aligners)

TophatIndexer (class in imfusion.build.indexers) TophatReference (class in imfusion.build.indexers) transcriptome_path (imfusion.build.indexers.TophatReference attribute) transposon_name (imfusion.build.indexers.Reference attribute) transposon_path (imfusion.build.indexers.Reference attribute)