Package: Platypus
Type: Package
Title: Single-Cell Immune Repertoire and Gene Expression Analysis
Description: 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
Date: 2024-10-17
Authors@R: c(person("Alexander", "Yermanos", role = c("aut", "cre"), email = "daphne.v.ginneken@gmail.com"),
             person("Andreas", "Agrafiotis", role = "ctb"),
             person("Victor", "Kreiner", role = "ctb"),
             person("Tudor-Stefan", "Cotet", role = "ctb"),
             person("Raphael", "Kuhn", role = "ctb"),
             person("Danielle", "Shlesinger", role = "ctb"),
             person("Jiami", "Han", role = "ctb"),
             person("Vittoria Martinolli", "D'Arcy", role = "ctb"),
             person("Lucas", "Stalder", role = "ctb"),
	     person("Daphne", "van Ginneken", role = "ctb"))
Maintainer: Alexander Yermanos <daphne.v.ginneken@gmail.com>
Depends: R(>= 4.0.0)
biocViews:
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),
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
LazyData: true
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2024-10-17 14:30:20 UTC; dginneke
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]
Repository: CRAN
Date/Publication: 2024-10-18 11:10:17 UTC
Built: R 4.4.3; ; 2025-11-26 05:42:14 UTC; windows
