Package index • isoformic

The IsoformicExperiment class

Transcript, gene and exon level data for the same samples, backed by Parquet files.

IsoformicExperiment(): IsoformicExperiment: Transcript, Gene and Exon Level Data in One Object
col_data() `col_data<-`() col_names() assays() assay_names() assay() `assay<-`() row_names() row_data() tx_annot() tx_to_gene() gene_assays() `gene_assays<-`() gene_assay() gene_names() gene_data() annot_data_transcripts() annot_data_genes() annot_data_exons() annot_data() annot_metadata() exon_table() clear_cache(): Accessors for IsoformicExperiment Objects
example_isoformic(): Example IsoformicExperiment

read_salmon(): Read Salmon Quantifications Into an IsoformicExperiment
read_oarfish(): Read Oarfish Quantifications Into an IsoformicExperiment
read_oarfish_sc_counts() read_oarfish_sc(): Read Oarfish single-cell quantifications
as_isoformic() as_summarized_experiment(): Convert Between IsoformicExperiment and SummarizedExperiment
write_isoformic() read_isoformic(): Save and Restore IsoformicExperiment Objects as Parquet

prepare_isoformic_annotation(): Convert a GFF3/GTF Annotation to Parquet Files
prepare_annotation(): Read a Prepared Annotation into Memory
prepare_exon_annotation(): Exon Table for Selected Genes From an Annotation
make_tx_to_gene(): Create a Transcript-to-Gene Mapping Table
merge_annotations(): Merge Per-Haplotype Annotations Into One Annotation Directory
add_annotation_columns(): Attach Extra Columns to the Annotation Tables
add_fantom_cat_tables(): Attach FANTOM CAT Tables to an Annotation
add_sqanti_classification(): Add SQANTI3 Structural Categories to an Annotation

download_reference(): Download Reference Annotations and Sequences
download_reference_url(): Download Any Reference File by URL
download_hprc_annotation(): Download HPRC Per-Haplotype CAT Annotations
download_fantom_cat_tables(): Download the FANTOM CAT Companion Tables
get_isoformic_cache(): Retrieve System-Dependent Cache Path for Isoformic
isoformic-options isoformic_options isoformic.frozen_mirrors: Options and environment variables used by isoformic

Inferential replicates, equivalence classes and run metadata from Salmon turned into uncertainty, ambiguity and confidence of isoform-level results.

read_inferential_replicates() equivalence_support() salmon_run_qc() inferential_replicates_table() as_inferential_replicates(): Read the inferential uncertainty that Salmon writes
add_uncertainty() tx_uncertainty() isoform_ambiguity() de_confidence() uncertainty_report() uncertainty_methods(): Quantify and report the uncertainty of isoform-level results
confidence_palette() plot_de_confidence() plot_isoform_correlation() plot_inf_rv(): Plot the uncertainty of isoform-level results
inferential_overdispersion() scale_counts(): Put the quantification uncertainty into the counts
read_terminus_groups(): Read the transcript groups that Terminus builds
run_terminus(): Run Terminus on Salmon output from R
read_treeterminus() cut_transcript_trees(): Read and cut the transcript trees of TreeTerminus
test_usage(): Test differential transcript usage

transcript_features() splicing_events(): Structural and Coding Features of Transcripts
extract_transcript_sequences() has_sequences() transcript_sequences(): Extract Transcript Sequences into an Annotation Directory
transcript_orfs() coding_potential(): Open Reading Frames of Transcripts from Their Sequences
productivity_palette() transcript_productivity() productive_fraction() productivity_fractions() test_productive_fraction() run_productivity_enrichment() poison_exons() benchmark_productivity(): Productivity of Transcripts and Genes
add_appris() add_riboseq_orfs() add_nmd_exons(): Attach External Productivity Evidence to an Annotation
domain_retention(): Protein Domain Retention of Isoforms
gtex_reference() gtex_tissues(): Tissue Reference Values from GTEx
polya_sites() read_polya_gff() apa_usage() test_apa(): Poly(A) Sites and Alternative Polyadenylation of Transcripts

Reference tables pinned to a source version (APPRIS, Ribo-seq ORFs, validated NMD exons, PolyASite, GTEx) and the coding potential model.

frozen_datasets() frozen_mirrors() fetch_frozen_data() read_frozen_data() bundle_frozen_data(): Frozen Reference Datasets
build_frozen_appris() build_frozen_appris_domains() build_frozen_riboseq_orfs() build_frozen_nmd_exons() build_frozen_polyasite() build_frozen_gtex(): Build the Frozen Datasets from Their Sources
build_coding_model(): Train the Coding Potential Model

de_tx() de_gene() `de_tx<-`() `de_gene<-`() de_cutoffs() `de_cutoffs<-`() de_table(): Differential Expression Results in an IsoformicExperiment
join_DEG_DET(): Merge Gene and Transcript Level Differential Expression Tables
is_deg_sig(): Flag Transcripts Whose Gene Is Differentially Expressed

isoform_fraction() tx_diversity() dominant_isoform() isoform_switches() exon_diversity() haplotype_summary(): Transcriptomic Diversity Summaries

plot_log2fc() plot_log2FC(): Plot Log2 Fold-Changes of a Gene and Its Isoforms
profile_data() plot_tx_expr(): Expression Profiles of Genes and Their Isoforms Across Groups
prepare_profile_data(): Prepare Expression Profile Data From Loose Tables
plot_genomic_context() plot_tx_context(): Plot the Genomic Context of a Gene's Isoforms
tx_type_palette(): Transcript Type Color Palette
productivity_palette() transcript_productivity() productive_fraction() productivity_fractions() test_productive_fraction() run_productivity_enrichment() poison_exons() benchmark_productivity(): Productivity of Transcripts and Genes

run_enrichment() default_enrichment_types() read_gmt() plot_enrichment(): Transcript-Type Aware Gene Set Enrichment

read_parquet() read_tabular() write_parquet(): Read and Write Parquet Files
summarize_to_gene(): Summarize Transcript-Level Matrices to Gene Level
salmon_index(): Build Salmon Index
salmon_quant(): Run Salmon Quantification