Package: immLynx 1.0.0
Nick Borcherding
immLynx: Linking Advanced TCR Python Pipelines and Hugging Face Models in R
A comprehensive toolkit that bridges popular Python-based immune repertoire analysis tools and Hugging Face protein language models into the R environment. Provides unified interfaces for TCR distance calculations (tcrdist3), sequence generation probability (OLGA), selection inference (soNNia), clustering (clusTCR), protein embeddings (ESM-2), metaclone discovery (metaclonotypist). Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.
Authors:
immLynx_1.0.0.tar.gz
immLynx_1.0.0.zip(r-4.7)immLynx_1.0.0.zip(r-4.6)immLynx_1.0.0.zip(r-4.5)
immLynx_1.0.0.tar.gz(r-4.7-any)immLynx_1.0.0.tar.gz(r-4.6-any)
immLynx_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
immLynx/json (API)
NEWS
| # Install 'immLynx' in R: |
| install.packages('immLynx', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/borchlab/immlynx/issues
- immLynx_example - Example Single-Cell RNA-seq Data with TCR Information
On BioConductor:immLynx-1.1.0(bioc 3.24)immLynx-1.0.0(bioc 3.23)
softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotationclusteringdimensionreduction
Last updated from:e2fd5794bf (on RELEASE_3_23). Checks:6 NOTE, 2 OK, 2 FAIL. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 203 | ||
| linux-devel-x86_64 | NOTE | 1110 | ||
| source / vignettes | OK | 259 | ||
| linux-release-x86_64 | NOTE | 1128 | ||
| macos-release-arm64 | FAIL | 3699 | ||
| macos-oldrel-arm64 | FAIL | 3709 | ||
| windows-devel | NOTE | 679 | ||
| windows-release | NOTE | 962 | ||
| windows-oldrel | NOTE | 595 | ||
| wasm-release | OK | 160 |
Exports:convertToTcrdistextractTCRdatagenerateOLGAhuggingModelproteinEmbeddingsrunClustTCRrunEmbeddingsrunHLAassociationrunMetaclonotypistrunOLGArunSoNNiarunTCRdistshowsummarizeTCRrepertoiretokenizeSequencesvalidateTCRdata
Dependencies:abindaskpassbasiliskBiobaseBiocGenericsBiostringsclicrayoncurlDelayedArraydir.expiryfilelockgenericsGenomicRangesglueherehttrimmApeximmReferentIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootrvestS4ArraysS4VectorsselectrSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbleutf8vctrswithrxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert TCR Data to tcrdist3 Format | convertToTcrdist |
| Extract TCR Data from SingleCellExperiment Object | extractTCRdata |
| Generate Random TCR Sequences using OLGA | generateOLGA |
| Initialize a Hugging Face Model and Tokenizer | huggingModel |
| Example Single-Cell RNA-seq Data with TCR Information | immLynx_example |
| Get Protein Embeddings from a Model | proteinEmbeddings |
| Run clusTCR Clustering on scRepertoire Data | runClustTCR |
| Generate Protein Language Model Embeddings for TCR Sequences | runEmbeddings |
| Perform HLA Association Analysis on Metaclones | runHLAassociation |
| Run Metaclonotypist for TCR Metaclone Discovery | runMetaclonotypist |
| Calculate Generation Probability (Pgen) for TCRs in scRepertoire Data | runOLGA |
| Run soNNia Selection Analysis | runSoNNia |
| Calculate TCR Distances on scRepertoire Data | runTCRdist |
| Summarize TCR Repertoire Statistics | summarizeTCRrepertoire |
| S4 Class for TCR Repertoire Summary | show,TCR_summary-method TCR_summary-class |
| Tokenize Amino Acid Sequences | tokenizeSequences |
| Validate TCR Data Format | validateTCRdata |
