Index

A

add_expression_to_genes() (in module GRATIOSA.useful_functions_transcriptome) add_genes() (GRATIOSA.TSS_TTS_TU.TSS method) (GRATIOSA.TSS_TTS_TU.TTS method) (GRATIOSA.TSS_TTS_TU.TU method)

add_prom_elements() (GRATIOSA.TSS_TTS_TU.TSS method) add_promoter() (GRATIOSA.TSS_TTS_TU.TSS method) add_TSS() (GRATIOSA.TSS_TTS_TU.TU method) add_TTS() (GRATIOSA.TSS_TTS_TU.TU method) add_TU_expression() (GRATIOSA.TSS_TTS_TU.TU method)

B

barplot_annotate_brackets() (in module GRATIOSA.plot_stat_analysis)

C

Chipseq (class in GRATIOSA.Chipseq) compute_fc_from_expr() (GRATIOSA.Transcriptome.Transcriptome method) compute_rpkm_from_cov() (GRATIOSA.Transcriptome.Transcriptome method)

compute_state_from_fc() (GRATIOSA.Transcriptome.Transcriptome method) cov_from_reads() (in module GRATIOSA.useful_functions_transcriptome) cov_start_stop_from_reads() (in module GRATIOSA.useful_functions_transcriptome) create_database() (GRATIOSA.Genome.Genome method)

D

data_classification() (in module GRATIOSA.stat_analysis)

E

enrichment_test() (in module GRATIOSA.stat_analysis)

G

Genome (class in GRATIOSA.Genome) get_all_signals() (GRATIOSA.Chipseq.Chipseq method) GO (class in GRATIOSA.GO) GRATIOSA.plot_genome module GRATIOSA.plot_stat_analysis module

GRATIOSA.stat_analysis module GRATIOSA.useful_functions_genome module GRATIOSA.useful_functions_HiC module GRATIOSA.useful_functions_transcriptome module

H

HiC (class in GRATIOSA.HiC)

L

load_annot_general() (in module GRATIOSA.useful_functions_genome) load_annotation() (GRATIOSA.Genome.Genome method) load_binned_signal() (GRATIOSA.Chipseq.Chipseq method) load_borders_genes() (GRATIOSA.HiC.HiC method) load_cov_start_end() (GRATIOSA.Transcriptome.Transcriptome method) load_expression() (GRATIOSA.Transcriptome.Transcriptome method) load_fc_pval() (GRATIOSA.Transcriptome.Transcriptome method) load_fc_pval_cond() (in module GRATIOSA.useful_functions_transcriptome) load_gene_orientation() (GRATIOSA.Genome.Genome method) load_genes_per_pos() (GRATIOSA.Genome.Genome method) load_gff() (in module GRATIOSA.useful_functions_genome) load_GO() (GRATIOSA.Genome.Genome method) load_hic_borders() (GRATIOSA.HiC.HiC method) load_hic_loops() (GRATIOSA.HiC.HiC method) load_HiC_site_cond() (in module GRATIOSA.useful_functions_HiC) load_loops_genes() (GRATIOSA.HiC.HiC method)

load_neighbor_all() (GRATIOSA.Genome.Genome method) load_peaks() (GRATIOSA.Chipseq.Chipseq method) load_pos_orientation() (GRATIOSA.Genome.Genome method) load_prom_elements() (GRATIOSA.Genome.Genome method) load_rnaseq_cov() (GRATIOSA.Transcriptome.Transcriptome method) load_seq() (GRATIOSA.Genome.Genome method) load_signal() (GRATIOSA.Chipseq.Chipseq method) load_signal_per_genes() (GRATIOSA.Chipseq.Chipseq method) load_signals_average() (GRATIOSA.Chipseq.Chipseq method) load_sites() (GRATIOSA.Genome.Genome method) load_smoothed_signal() (GRATIOSA.Chipseq.Chipseq method) load_TSS() (GRATIOSA.Genome.Genome method) load_TSS_cond() (in module GRATIOSA.useful_functions_genome) load_TTS() (GRATIOSA.Genome.Genome method) load_TTS_cond() (in module GRATIOSA.useful_functions_genome) load_TU() (GRATIOSA.Genome.Genome method) load_TU_cond() (in module GRATIOSA.useful_functions_genome)

M

module GRATIOSA.plot_genome GRATIOSA.plot_stat_analysis GRATIOSA.stat_analysis GRATIOSA.useful_functions_genome GRATIOSA.useful_functions_HiC GRATIOSA.useful_functions_transcriptome

P

plot_enrichment_test() (in module GRATIOSA.plot_stat_analysis) plot_proportion_test() (in module GRATIOSA.plot_stat_analysis) plot_region() (in module GRATIOSA.plot_genome)

plot_student_test() (in module GRATIOSA.plot_stat_analysis) process_bam() (in module GRATIOSA.useful_functions_transcriptome) proportion_test() (in module GRATIOSA.stat_analysis)

Q

quantitative_data_student_test() (in module GRATIOSA.stat_analysis)

R

read_seq() (in module GRATIOSA.useful_functions_genome)

S

significance() (in module GRATIOSA.plot_stat_analysis) subplot_genes() (in module GRATIOSA.plot_genome)

subplot_rnaseq_coverage() (in module GRATIOSA.plot_genome) subplot_signal() (in module GRATIOSA.plot_genome)

T

Transcriptome (class in GRATIOSA.Transcriptome) TSS (class in GRATIOSA.TSS_TTS_TU)

TTS (class in GRATIOSA.TSS_TTS_TU) TU (class in GRATIOSA.TSS_TTS_TU)

U

update_NCBI_genomes() (in module GRATIOSA.useful_functions_genome)