We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.
| Version: | 3.6.0 |
| Depends: | R (≥ 4.0.0) |
| Imports: | Biostrings,cowplot,dplyr,ggalluvial,ggplot2,ggseqlogo,ggtree,jsonlite,knitr,magrittr,Matrix (≥ 1.3-3),plyr,reshape2,seqinr,Seurat,SeuratObject (≥ 4.1.3),stringdist,stringr,tibble,tidyr, utils,useful |
| Suggests: | AnnotationDbi,ape,BiocGenerics,biomaRt,circlize,cluster,doParallel,fgsea,ggrepel,ggridges,gridExtra,harmony,igraph,iNEXT,limma,kmer,msigdbr,phangorn,pheatmap,phytools,purrr,readr,readxl,rstudioapi,Rtsne,scales,sf,SingleCellExperiment,slingshot,tidytree,tidyselect,tidyverse,umap,vegan,viridis,testthat (≥ 3.0.0) |
| Published: | 2024-10-18 |
| DOI: | 10.32614/CRAN.package.Platypus |
| Author: | Alexander Yermanos [aut, cre], Andreas Agrafiotis [ctb], Victor Kreiner [ctb], Tudor-Stefan Cotet [ctb], Raphael Kuhn [ctb], Danielle Shlesinger [ctb], Jiami Han [ctb], Vittoria Martinolli D'Arcy [ctb], Lucas Stalder [ctb], Daphne van Ginneken [ctb] |
| Maintainer: | Alexander Yermanos <daphne.v.ginneken at gmail.com> |
| License: | GPL-2 |
| NeedsCompilation: | no |
| Materials: | README,NEWS |
| CRAN checks: | Platypus results[issues need fixing before 2026-01-12] |