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 |