Index

_

__contains__() (isotools.Transcriptome method)

__getitem__() (isotools.Transcriptome method) __len__() (isotools.Transcriptome method)

A

add_annotation_domains() (isotools.Transcriptome method) add_direct_repeat_len() (isotools.Gene method) add_domains_to_table() (in module isotools.domains) add_filter() (isotools.Transcriptome method) add_fragments() (isotools.Gene method) add_hmmer_domains() (isotools.Transcriptome method) add_interpro_domains() (isotools.Gene method) add_noncanonical_splicing() (isotools.Gene method) add_orfs() (isotools.Gene method)

add_qc_metrics() (isotools.Transcriptome method) add_sample_from_bam() (isotools.Transcriptome method) add_sample_from_csv() (isotools.Transcriptome method) add_short_read_coverage() (isotools.Transcriptome method) add_threeprime_a_content() (isotools.Gene method) alternative_splicing_events() (isotools.Transcriptome method) altsplice_stats() (isotools.Transcriptome method) altsplice_test() (isotools.Transcriptome method) ANNOTATION_VOCABULARY (in module isotools)

C

chimeric_table() (isotools.Transcriptome method) chrom (isotools.Gene property) chromosomes (isotools.Transcriptome property) coding_len() (isotools.Gene method) collapse_immune_genes() (isotools.Transcriptome method)

coordination_test() (isotools.Gene method) (isotools.Transcriptome method) copy() (isotools.Gene method) correct_fuzzy_junctions() (isotools.Gene method) coverage (isotools.Gene property)

D

DEFAULT_GENE_FILTER (in module isotools) DEFAULT_REF_TRANSCRIPT_FILTER (in module isotools) DEFAULT_TRANSCRIPT_FILTER (in module isotools)

die_test() (isotools.Gene method) (isotools.Transcriptome method) direct_repeat_hist() (isotools.Transcriptome method) downstream_a_hist() (isotools.Transcriptome method)

E

end (isotools.SegGraphNode property) events_dist() (isotools.SegmentGraph method)

exons_per_transcript_hist() (isotools.Transcriptome method) export_alternative_splicing() (isotools.Transcriptome method)

F

filter_stats() (isotools.Transcriptome method) find_fragments() (isotools.SegmentGraph method) find_splice_bubbles() (isotools.SegmentGraph method)

find_splice_sites() (isotools.SegmentGraph method) find_transcript_positions() (isotools.Gene method) from_reference() (isotools.Transcriptome class method) fuzzy_junction() (isotools.SegmentGraph method)

G

Gene (class in isotools) gene_coverage (isotools.Gene property) gene_table() (isotools.Transcriptome method) gene_track() (isotools.Gene method) get_all_orf() (isotools.Gene method) get_alternative_splicing() (isotools.SegmentGraph method) get_exon_support_matrix() (isotools.SegmentGraph method)

get_infos() (isotools.Gene method) get_intersects() (isotools.SegmentGraph method) get_intron_support_matrix() (isotools.SegmentGraph method) get_node_matrix() (isotools.SegmentGraph method) get_overlap() (isotools.SegmentGraph method) get_sequence() (isotools.Gene method) groups() (isotools.Transcriptome method)

I

id (isotools.Gene property) import_hmmer_models() (in module isotools.domains) is_annotated (isotools.Gene property) is_exonic() (isotools.SegmentGraph method) is_expressed (isotools.Gene property) isotools module

isotools.domains module isotools.plots module iter_genes() (isotools.Transcriptome method) iter_ref_transcripts() (isotools.Transcriptome method) iter_transcripts() (isotools.Transcriptome method)

L

load() (isotools.Transcriptome class method)

M

make_index() (isotools.Transcriptome method) module isotools isotools.domains isotools.plots

N

n_genes (isotools.Transcriptome property) n_ref_transcripts (isotools.Gene property) n_transcripts (isotools.Gene property) (isotools.Transcriptome property)

name (isotools.Gene property) novel_genes (isotools.Transcriptome property)

P

plot_bar() (in module isotools.plots) plot_diff_results() (in module isotools.plots) plot_distr() (in module isotools.plots) plot_domains() (isotools.Gene method)

plot_embedding() (in module isotools.plots) plot_rarefaction() (in module isotools.plots) plot_saturation() (in module isotools.plots) pre (isotools.SegGraphNode property)

R

rarefaction() (isotools.Transcriptome method) ref_segment_graph (isotools.Gene property) ref_transcripts (isotools.Gene property) region (isotools.Gene property)

remove_chromosome() (isotools.Transcriptome method) remove_filter() (isotools.Transcriptome method) remove_samples() (isotools.Transcriptome method) remove_short_read_coverage() (isotools.Transcriptome method)

S

sample_table (isotools.Transcriptome property) samples (isotools.Transcriptome property) sashimi_figure() (isotools.Gene method) sashimi_plot() (isotools.Gene method) sashimi_plot_short_reads() (isotools.Gene method) save() (isotools.Transcriptome method) save_reference() (isotools.Transcriptome method) search_transcript() (isotools.SegmentGraph method)

search_transcript2() (isotools.SegmentGraph method) SegGraphNode (class in isotools) segment_graph (isotools.Gene property) SegmentGraph (class in isotools) short_reads() (isotools.Gene method) SPLICE_CATEGORY (in module isotools) start (isotools.SegGraphNode property) strand (isotools.Gene property) suc (isotools.SegGraphNode property)

T

tpm() (isotools.Gene method) transcript_coverage_hist() (isotools.Transcriptome method) transcript_length_hist() (isotools.Transcriptome method)

transcript_table() (isotools.Transcriptome method) Transcriptome (class in isotools) transcripts (isotools.Gene property) transcripts_per_gene_hist() (isotools.Transcriptome method)

W

write_gtf() (isotools.Transcriptome method)