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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 |
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These binaries (installable software) and packages are in development.
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