Package index • IDConverter

ID Conversion

Convert identifiers within or between biological databases.

convert_tcga(): Convert TCGA Identifiers
convert_icgc(): Convert ICGC Identifiers
convert_pcawg(): Convert PCAWG Identifiers
convert_custom(): Convert Identifiers with Custom Database
convert_hm_genes(): Convert Gene IDs between Ensembl and Hugo Symbol System
convert_hm_orthologs(): Convert Gene IDs Between Human and Mouse via Orthology

Gene Annotation Tables

Build, load, and manage gene annotation tables from Ensembl or Zenodo.

build_annotables(): Build Gene Annotation Tables from Ensembl BioMart
load_data(): Load Data from Local or Remote Zenodo Repository
ls_annotables(): List Available Annotation Tables
resolve_gene_aliases(): Resolve Gene Symbol Aliases

GDC / TCGA Utilities

Parse GDC manifest files, pair tumor-normal samples, and filter barcodes.

parse_gdc_file_uuid(): Parse Sample ID from GDC Portal File UUID
pair_gdc_samples(): Pair Tumor-Normal Samples from GDC Manifest
filter_tcga_barcodes(): Filter TCGA Replicate Sample Barcodes

Datasets

Bundled identifier mapping datasets for offline use.

tcga: TCGA Case Identifiers
icgc: ICGC Sample Identifiers
pcawg_full: PCAWG Full Sample Identifiers
pcawg_simple: PCAWG Mutation Related Simplified Sample Identifiers