Overview | ID Conversion | Gene ID Conversion | Gene Annotation Tables | Working with Custom Databases
Package: IDConverter 0.4.0
Shixiang Wang
IDConverter: Convert Identifiers in Biological Databases
Identifiers in biological databases connect different levels of metadata, phenotype data or genotype data. This tool is designed to easily convert identifiers within or between different biological databases (Wang, Shixiang, et al. (2021) <doi:10.1371/journal.pgen.1009557>).
Authors:
IDConverter_0.4.0.tar.gz
IDConverter_0.4.0.zip(r-4.7-any)
IDConverter_0.4.0.tar.gz(r-4.7-any)IDConverter_0.4.0.tar.gz(r-4.6-any)
IDConverter_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IDConverter/json (API)
| # Install 'IDConverter' in R: |
| install.packages('IDConverter', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wanglabcsu/idconverter/issues
Pkgdown/docs site:https://wanglabcsu.github.io
Datasets:
- icgc - ICGC Sample Identifiers
- pcawg_full - PCAWG Full Sample Identifiers
- pcawg_simple - PCAWG Mutation Related Simplified Sample Identifiers
- tcga - TCGA Case Identifiers
Last updated from:fbd5fe64ce. Checks:5 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 181 | ||
| source / vignettes | OK | 239 | ||
| linux-release-x86_64 | OK | 174 | ||
| windows-devel-x86_64 | OK | 134 | ||
| wasm-release | OK | 144 |
Exports:build_annotablesconvert_customconvert_hm_genesconvert_hm_orthologsconvert_icgcconvert_pcawgconvert_tcgafilter_tcga_barcodesload_datals_annotablespair_gdc_samplesparse_gdc_file_uuidresolve_gene_aliases
Dependencies:askpassclicurldata.tablegluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangsystibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build Gene Annotation Tables from Ensembl BioMart | build_annotables |
| Convert Identifiers with Custom Database | convert_custom |
| Convert Gene IDs between Ensembl and Hugo Symbol System | convert_hm_genes |
| Convert Gene IDs Between Human and Mouse via Orthology | convert_hm_orthologs |
| Convert ICGC Identifiers | convert_icgc |
| Convert PCAWG Identifiers | convert_pcawg |
| Convert TCGA Identifiers | convert_tcga |
| Filter TCGA Replicate Sample Barcodes | filter_tcga_barcodes |
| ICGC Sample Identifiers | icgc |
| Load Data from Local or Remote Zenodo Repository | load_data |
| List Available Annotation Tables | ls_annotables |
| Pair Tumor-Normal Samples from GDC Manifest | pair_gdc_samples |
| Parse Sample ID from GDC Portal File UUID | parse_gdc_file_uuid |
| PCAWG Full Sample Identifiers | pcawg_full |
| PCAWG Mutation Related Simplified Sample Identifiers | pcawg_simple |
| Resolve Gene Symbol Aliases | resolve_gene_aliases |
| TCGA Case Identifiers | tcga |
