Index

_

__init__() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.fastq.PairedEndPipeline method) (rnalysis.fastq.SingleEndPipeline method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) (rnalysis.filtering.Pipeline method)

A

add() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) add_function() (rnalysis.fastq.PairedEndPipeline method) (rnalysis.fastq.SingleEndPipeline method) (rnalysis.filtering.Pipeline method)

apply_to() (rnalysis.fastq.PairedEndPipeline method) (rnalysis.fastq.SingleEndPipeline method) (rnalysis.filtering.Pipeline method) Attribute Reference Table average_replicate_samples() (rnalysis.filtering.CountFilter method)

B

Biotype Reference Table biotypes_from_gtf() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) biotypes_from_ref_table() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

bowtie2_align_paired_end() (in module rnalysis.fastq) bowtie2_align_single_end() (in module rnalysis.fastq) bowtie2_create_index() (in module rnalysis.fastq) box_plot() (rnalysis.filtering.CountFilter method)

C

change_set_name() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) clear() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) clear_all_cache() (in module rnalysis.general) clear_gui_cache() (in module rnalysis.general) clustergram() (rnalysis.filtering.CountFilter method) concatenate() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

convert_sam_format() (in module rnalysis.fastq) copy() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) CountFilter (class in rnalysis.filtering) create_bam_index() (in module rnalysis.fastq)

D

describe() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) DESeqFilter (class in rnalysis.filtering) difference() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

difference_update() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) differential_expression_deseq2() (rnalysis.filtering.CountFilter method) differential_expression_deseq2_simplified() (rnalysis.filtering.CountFilter method) differential_expression_limma_voom() (rnalysis.filtering.CountFilter method) differential_expression_limma_voom_simplified() (rnalysis.filtering.CountFilter method) discard() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) drop_columns() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

E

enhanced_box_plot() (rnalysis.filtering.CountFilter method) enrichment_bar_plot() (in module rnalysis.enrichment)

export_pipeline() (rnalysis.fastq.PairedEndPipeline method) (rnalysis.fastq.SingleEndPipeline method) (rnalysis.filtering.Pipeline method)

F

fastq_to_sam_paired() (in module rnalysis.fastq) fastq_to_sam_single() (in module rnalysis.fastq) featurecounts_paired_end() (in module rnalysis.fastq) featurecounts_single_end() (in module rnalysis.fastq) FeatureSet (class in rnalysis.enrichment) Filter (class in rnalysis.filtering) Filter object Filter objects filter_abs_log2_fold_change() (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.FoldChangeFilter method) filter_biotype_from_gtf() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_biotype_from_ref_table() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_by_attribute() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_by_go_annotations() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_by_kegg_annotations() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_by_row_name() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

filter_by_row_sum() (rnalysis.filtering.CountFilter method) filter_duplicate_ids() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_fold_change_direction() (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.FoldChangeFilter method) filter_low_reads() (rnalysis.filtering.CountFilter method) filter_missing_values() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_percentile() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) filter_significant() (rnalysis.filtering.DESeqFilter method) filter_top_n() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) find_duplicates() (in module rnalysis.fastq) find_paralogs_ensembl() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) find_paralogs_panther() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) fold_change() (rnalysis.filtering.CountFilter method) FoldChangeFilter (class in rnalysis.filtering) from_dataframe() (rnalysis.filtering.CountFilter class method) (rnalysis.filtering.DESeqFilter class method) (rnalysis.filtering.Filter class method) (rnalysis.filtering.FoldChangeFilter class method) from_folder() (rnalysis.filtering.CountFilter class method) from_folder_htseqcount() (rnalysis.filtering.CountFilter class method)

G

gene_ontology_graph() (in module rnalysis.enrichment)

go_enrichment() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method)

H

head() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

histogram() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

I

import_pipeline() (rnalysis.fastq.PairedEndPipeline class method) (rnalysis.fastq.SingleEndPipeline class method) (rnalysis.filtering.Pipeline class method) intersection() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

intersection_update() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) isdisjoint() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) issubset() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) issuperset() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method)

K

kallisto_create_index() (in module rnalysis.fastq) kallisto_quantify_paired_end() (in module rnalysis.fastq) kallisto_quantify_single_end() (in module rnalysis.fastq)

kegg_enrichment() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) kegg_pathway_graph() (in module rnalysis.enrichment)

M

ma_plot() (rnalysis.filtering.CountFilter method) majority_vote_intersection() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) map_orthologs_ensembl() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) map_orthologs_orthoinspector() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

map_orthologs_panther() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) map_orthologs_phylomedb() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) module rnalysis.enrichment rnalysis.fastq rnalysis.filtering rnalysis.general

N

non_categorical_enrichment() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) normalize_median_of_ratios() (rnalysis.filtering.CountFilter method) normalize_rle() (rnalysis.filtering.CountFilter method) normalize_tmm() (rnalysis.filtering.CountFilter method) normalize_to_quantile() (rnalysis.filtering.CountFilter method) normalize_to_rpkm() (rnalysis.filtering.CountFilter method)

normalize_to_rpm() (rnalysis.filtering.CountFilter method) normalize_to_rpm_htseqcount() (rnalysis.filtering.CountFilter method) normalize_to_tpm() (rnalysis.filtering.CountFilter method) normalize_with_scaling_factors() (rnalysis.filtering.CountFilter method) number_filters() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

P

PairedEndPipeline (class in rnalysis.fastq) pairplot() (rnalysis.filtering.CountFilter method) parse_gene_name_string() (in module rnalysis.general) parse_sequence_name_string() (in module rnalysis.general) parse_wbgene_string() (in module rnalysis.general) pca() (rnalysis.filtering.CountFilter method) Pipeline (class in rnalysis.filtering)

plot_expression() (rnalysis.filtering.CountFilter method) pop() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) print_features() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) print_settings_file() (in module rnalysis.general) pval_histogram() (rnalysis.filtering.DESeqFilter method)

R

randomization_test() (rnalysis.filtering.FoldChangeFilter method) RankedSet (class in rnalysis.enrichment) remove() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) remove_last_function() (rnalysis.fastq.PairedEndPipeline method) (rnalysis.fastq.SingleEndPipeline method) (rnalysis.filtering.Pipeline method)

reset_settings_file() (in module rnalysis.general) rnalysis.enrichment module rnalysis.fastq module rnalysis.filtering module rnalysis.general module

S

sam_to_fastq_paired() (in module rnalysis.fastq) sam_to_fastq_single() (in module rnalysis.fastq) save_csv() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) save_parquet() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) save_table() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) save_to_csv() (in module rnalysis.general) save_txt() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) scatter_sample_vs_sample() (rnalysis.filtering.CountFilter method) set_attr_ref_table_path() (in module rnalysis.general) set_biotype_ref_table_path() (in module rnalysis.general) shortstack_align_smallrna() (in module rnalysis.fastq) single_set_enrichment() (rnalysis.enrichment.RankedSet method) single_set_go_enrichment() (rnalysis.enrichment.RankedSet method) single_set_kegg_enrichment() (rnalysis.enrichment.RankedSet method) SingleEndPipeline (class in rnalysis.fastq) sort() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

sort_by_principal_component() (rnalysis.filtering.CountFilter method) sort_sam() (in module rnalysis.fastq) split_by_attribute() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) split_by_percentile() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) split_by_principal_components() (rnalysis.filtering.CountFilter method) split_by_reads() (rnalysis.filtering.CountFilter method) split_clicom() (rnalysis.filtering.CountFilter method) split_fold_change_direction() (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.FoldChangeFilter method) split_hdbscan() (rnalysis.filtering.CountFilter method) split_hierarchical() (rnalysis.filtering.CountFilter method) split_kmeans() (rnalysis.filtering.CountFilter method) split_kmedoids() (rnalysis.filtering.CountFilter method) symmetric_difference() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) symmetric_difference_update() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method)

T

tail() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) text_filters() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) transform() (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

translate_gene_ids() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method) trim_adapters_paired_end() (in module rnalysis.fastq) trim_adapters_single_end() (in module rnalysis.fastq)

U

union() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) (rnalysis.filtering.CountFilter method) (rnalysis.filtering.DESeqFilter method) (rnalysis.filtering.Filter method) (rnalysis.filtering.FoldChangeFilter method)

update() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method) upset_plot() (in module rnalysis.enrichment) user_defined_enrichment() (rnalysis.enrichment.FeatureSet method) (rnalysis.enrichment.RankedSet method)

V

validate_sam() (in module rnalysis.fastq) venn_diagram() (in module rnalysis.enrichment)

violin_plot() (rnalysis.filtering.CountFilter method) volcano_plot() (rnalysis.filtering.DESeqFilter method)