Package: immReferent 1.1.0
Nick Borcherding
immReferent: An Interface for Immune Receptor and HLA Gene Reference Data
Provides a consistent interface for downloading, storing, and accessing immune receptor (TCR/BCR) and HLA sequences from IMGT, IPD-IMGT/HLA, and OGRDB (AIRR-C). Supports export to popular analysis tools including MiXCR, TRUST4, Cell Ranger, and IgBLAST. This package serves as a core dependency for immunogenomics packages, ensuring reliable and high-quality sequence access with local caching for reproducibility.
Authors:
immReferent_1.1.0.tar.gz
immReferent_1.1.0.zip(r-4.7)immReferent_1.1.0.zip(r-4.6)immReferent_1.1.0.zip(r-4.5)
immReferent_1.1.0.tgz(r-4.6-any)immReferent_1.1.0.tgz(r-4.5-any)
immReferent_1.1.0.tar.gz(r-4.7-any)immReferent_1.1.0.tar.gz(r-4.6-any)
immReferent_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
immReferent/json (API)
NEWS
| # Install 'immReferent' in R: |
| install.packages('immReferent', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/borchlab/immreferent/issues
On BioConductor:immReferent-1.1.0(bioc 3.24)immReferent-1.0.0(bioc 3.23)
Last updated from:ec8d075a73. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 166 | ||
| linux-devel-x86_64 | OK | 269 | ||
| source / vignettes | OK | 267 | ||
| linux-release-x86_64 | OK | 257 | ||
| macos-release-arm64 | OK | 189 | ||
| macos-oldrel-arm64 | OK | 215 | ||
| windows-devel | OK | 160 | ||
| windows-release | OK | 188 | ||
| windows-oldrel | OK | 181 | ||
| wasm-release | OK | 115 |
Exports:exportCellRangerexportIgBLASTexportMiXCRexportTRUST4getIMGTgetOGRDBis_imgt_availableis_ogrdb_availablelistIMGTlistOGRDBloadIMGTloadOGRDBrefreshIMGTrefreshOGRDB
Dependencies:askpassBiocGenericsBiostringsclicrayoncurlgenericsgluehttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigR6rlangrvestS4VectorsselectrSeqinfostringistringrsystibbleutf8vctrsxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| immReferent: An Interface for Immune Receptor and HLA Gene Reference Data | immReferent-package immReferent |
| Export Reference Sequences to Cell Ranger VDJ Format | exportCellRanger |
| Export Reference Sequences to IgBLAST Format | exportIgBLAST |
| Export Reference Sequences to MiXCR Format | exportMiXCR |
| Export Reference Sequences to TRUST4 Format | exportTRUST4 |
| Download and Load Immune Receptor and HLA Sequences from IMGT | getIMGT |
| Download and Load Immune Receptor Germline Sequences from OGRDB | getOGRDB |
| Check if IMGT Website is Available | is_imgt_available |
| Check if OGRDB Website is Available | is_ogrdb_available |
| List Datasets in the Local Cache | listIMGT |
| List OGRDB Datasets in Local Cache | listOGRDB |
| Load Cached IMGT/HLA Sequences | loadIMGT |
| Load Cached OGRDB Sequences | loadOGRDB |
| Force Re-download of IMGT/HLA Sequences | refreshIMGT |
| Force Re-download of OGRDB Sequences | refreshOGRDB |
