├── .Rbuildignore ├── .github ├── .gitignore ├── .gitkeep ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md └── workflows │ ├── .gitkeep │ ├── pkgdown.yaml │ └── r-cmd-check.yaml ├── .gitignore ├── .markdownlint-cli2.jsonc ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── ContextData-class.R ├── IsoformicExperiment-class.R ├── as_isoformic.R ├── check_installed.R ├── convert_to_isoformic_tibble.R ├── download_reference.R ├── duckdb_run.R ├── extract_attribute.R ├── get_annot_metadata.R ├── get_isoformic_cache.R ├── is_deg_sig.R ├── isoformic-package.R ├── join_DEG_DET.R ├── make_tx_to_gene.R ├── parse_annot_attributes.R ├── plot_genomic_context.R ├── plot_log2FC.R ├── plot_tx_context.R ├── prepare_annotation.R ├── prepare_annotation_db.R ├── prepare_exon_annotation.R ├── prepare_isoformic_annotation.R ├── prepare_profile_data.R ├── profile_plot.R ├── run_enrichment.R ├── salmon_utils.R ├── summarize_to_gene.R └── tx_type_palette.R ├── README.md ├── _pkgdown.yml ├── data-raw └── .gitkeep ├── inst └── extdata │ ├── DEGs_PE_fixed2.csv │ ├── DETs_fixed.csv │ ├── PE_1_DETs.csv │ ├── PE_1_counts.csv │ ├── c2.cp.reactome.v2023.1.Hs.symbols.gmt.txt │ ├── example_gencode.v34.annotation.parquet │ ├── hsapiens_REAC_subset.gmt │ ├── isoformic-logo.png │ ├── mini_inf_reps.rds │ └── mini_quants │ ├── SRR11498039_quant │ ├── aux_info │ │ ├── ambig_info.tsv │ │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ │ └── salmon_quant.log │ └── quant.sf │ ├── SRR11498040_quant │ ├── aux_info │ │ ├── ambig_info.tsv │ │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ │ └── salmon_quant.log │ └── quant.sf │ ├── SRR11498041_quant │ ├── aux_info │ │ ├── ambig_info.tsv │ │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ │ └── salmon_quant.log │ └── quant.sf │ ├── SRR11498079_quant │ ├── aux_info │ │ ├── ambig_info.tsv │ │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ │ └── salmon_quant.log │ └── quant.sf │ ├── SRR11498080_quant │ ├── aux_info │ │ ├── ambig_info.tsv │ │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ │ └── salmon_quant.log │ └── quant.sf │ └── SRR11498081_quant │ ├── aux_info │ ├── ambig_info.tsv │ └── meta_info.json │ ├── cmd_info.json │ ├── keep_tx_used.txt │ ├── libParams │ └── flenDist.txt │ ├── lib_format_counts.json │ ├── logs │ └── salmon_quant.log │ └── quant.sf ├── justfile ├── man ├── ContextData.Rd ├── IsoformicExperiment.Rd ├── as_isoformic.Rd ├── create_context_data.Rd ├── download_reference.Rd ├── figures │ └── logo.png ├── get_isoformic_cache.Rd ├── is_deg_sig.Rd ├── isoformic-package.Rd ├── join_DEG_DET.Rd ├── make_tx_to_gene.Rd ├── plot_genomic_context.Rd ├── plot_log2FC.Rd ├── plot_tx_context.Rd ├── plot_tx_expr.Rd ├── prepare_annotation.Rd ├── prepare_annotation_db.Rd ├── prepare_exon_annotation.Rd ├── prepare_isoformic_annotation.Rd ├── prepare_profile_data.Rd ├── run_enrichment.Rd ├── salmon_index.Rd ├── salmon_quant.Rd └── tx_type_palette.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon.png │ ├── favicon-96x96.png │ ├── favicon.ico │ ├── favicon.svg │ ├── site.webmanifest │ ├── web-app-manifest-192x192.png │ └── web-app-manifest-512x512.png ├── tests ├── testthat.R └── testthat │ ├── setup.R │ ├── test-IsoformicExperiment.R │ ├── test-check_installed.R │ ├── test-download_reference.R │ └── test-set_random_experiment_name.R └── vignettes ├── .gitignore ├── articles ├── .gitignore └── .gitkeep ├── isoformic-preprocess.qmd ├── isoformic-table-based.qmd └── library.bib /.Rbuildignore: 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