scRepertoire - A toolkit for single-cell immune receptor profiling
scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R single-cell workflows.
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softwareimmunooncologysinglecellclassificationannotationsequencingcpp
9.89 score 376 stars 2 dependents 4 scripts 1.7k downloadsescape - Easy single cell analysis platform for enrichment
A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells. Alternatively, escape supports use of rank-based GSEA, such as the use of differential gene expression via fgsea.
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softwaresinglecellclassificationannotationgenesetenrichmentsequencinggenesignalingpathways
9.52 score 237 stars 1 dependents 269 scripts 1.1k downloadsimmApex - Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
A set of tools to for machine and deep learning in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.
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softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotationcppopenmp
7.20 score 15 stars 5 dependents 901 downloadsIbex - Methods for BCR single-cell embedding
Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects.
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softwareimmunooncologysinglecellclassificationannotationsequencing
6.84 score 28 stars 33 scripts 234 downloadsimmReferent - 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.
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softwareannotationsequencing
6.81 score 9 stars 6 dependents 6 scripts 296 downloadsimmLynx - 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.
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softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotationclusteringdimensionreduction
5.59 score 3 stars 6 scripts 296 downloadsimmGLIPH - Grouping of Lymphocyte Interactions by Paratope Hotspots
An R implementation of the GLIPH and GLIPH2 algorithms for clustering T cell receptors (TCRs) predicted to bind the same HLA-restricted peptide antigen. Identifies specificity groups based on local (motif-based) and global (sequence-based) CDR3 similarities. Integrates with the scRepertoire ecosystem via immApex for single-cell immune repertoire analysis. Users should cite the original GLIPH algorithm papers: Glanville et al. (2017) <doi:10.1038/nature22976> and Huang et al. (2020) <doi:10.1038/s41587-020-0505-4>.
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softwareimmunooncologyclusteringsinglecellsequencingvisualization
5.32 score 6 stars 7 scripts 410 downloads
bHIVE - B-cell Hybrid Immune Variant Engine
bHIVE implements an artificial immune network (AI-Net) for clustering and classification of high-dimensional data such as mass cytometry and single-cell profiles. A population of prototypes, called antibodies, evolves by clonal selection, somatic hypermutation and network suppression, and the learned prototypes summarize cell populations in the original marker units. The same fitted model clusters a dataset and labels new cells. bHIVE accepts SummarizedExperiment and SingleCellExperiment objects and integrates with bluster through bHIVEParam. A C++ backend computes affinities, mutations and suppression, and optional R6 modules add mechanisms such as germinal center selection, microenvironment-dependent mutation and isotype switching. The package also provides multilayer clustering, grid search and caret model wrappers.
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softwareclusteringclassificationsinglecellflowcytometrycellbasedassaysnetworkopenblascpp
3.85 score 10 scripts