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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 |
| Reference manual: | Platypus.pdf |
| Vignettes: |
PlatypusV3 AgedCNS vignette (source, R code) |
| Package source: | Platypus_3.6.0.tar.gz |
| Windows binaries: | r-devel: Platypus_3.6.0.zip, r-release: Platypus_3.6.0.zip, r-oldrel: Platypus_3.6.0.zip |
| macOS binaries: | r-release (arm64): Platypus_3.6.0.tgz, r-oldrel (arm64): Platypus_3.6.0.tgz, r-release (x86_64): Platypus_3.6.0.tgz, r-oldrel (x86_64): Platypus_3.6.0.tgz |
| Old sources: | Platypus archive |
Please use the canonical form https://CRAN.R-project.org/package=Platypus to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.