Package index • isoformic

All functions

IsoformicExperiment() col_data() annot_data_transcripts() annot_data_genes() annot_data_exons() annot_data() annot_row_names() col_names() row_names() tx_to_gene() tx_annot() de_tx() de_gene(): IsoformicExperiment Class

as_isoformic(): Convert a SummarizedExperiment to an IsoformicExperiment Object

create_context_data(): Create ContextData Object

download_reference(): Download Reference Files from GENCODE

get_isoformic_cache(): Retrieve System-Dependent Cache Path for Isoformic

is_deg_sig(): Annotate Transcripts with Differential Gene Expression Significance

join_DEG_DET(): Merge Gene and Transcript Level Differential Expression Tables

make_tx_to_gene(): Create Transcript-to-Gene Relationship Table

plot_genomic_context(): Plot Transcripts Genomic Context

plot_log2FC(): Plot Log2 Fold-Change Results for Transcripts of Selected Genes

plot_tx_context(): Plot Transcript Genomic Context

plot_tx_expr(): Plot Transcript per gene expression

prepare_annotation(): Prepare Annotation

prepare_annotation_db(): Write Parquet File from GFF

prepare_exon_annotation(): Prepare Exon based Position Annotation Table

prepare_isoformic_annotation(): Write Feature Annotation to Parquet Files

prepare_profile_data(): Prepare Data for Gene and Transcript Expression Profile Plot

run_enrichment(): Run Gene Set Enrichment Analysis for Different Transcript Types

tx_type_palette(): Transcript Type Color Palette