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, Omniscope, 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 workflows.
Last updated 27 days ago
softwareimmunooncologysinglecellclassificationannotationsequencing
9.69 score 308 stars 202 scripts 928 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.
Last updated 27 days ago
softwaresinglecellclassificationannotationgenesetenrichmentsequencinggenesignalingpathways
5.96 score 151 scripts 738 downloadsimmApex - Tools for Adaptive Immune Receptor Sequence-Based Keras Modeling
A set of tools to build tensorflow/keras3-based models 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.
Last updated 25 days ago
softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotation
4.88 score 8 stars 3 scripts