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 (Yermanos A, et al (2021) <doi:10.1093/nargab/lqab023>). 
Version: 3.4.1
Date: 2022-03-01
Authors@R: c(person("Alexander", "Yermanos", role = c("aut", "cre"), email = "ayermanos@gmail.com"),
             person("Andreas", "Agrafiotis", role = "ctb"),
             person("Raphael", "Kuhn", role = "ctb"),
	     person("Danielle", "Shlesinger", role = "ctb"),
             person("Jiami","Han", role = "ctb"),
             person("Tudor-Stefan","Cotet", role = "ctb"),
	     person("Victor", "Kreiner", role = "ctb"))
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Depends: R(>= 3.5.0),
Imports: BiocGenerics, Biostrings, cowplot, dplyr, ggplot2, ggtree,
        jsonlite, Matrix(>= 1.3-3), doParallel, foreach, plyr,
        reshape2, seqinr, stringr, Seurat, SeuratObject, tibble, tidyr,
        utils, useful
Suggests: AnnotationDbi, ape, bigstatsr, bio3d, Biobase, biomaRt,
        caret, circlize, colorspace, data.table, dichromat, e1071,
        edgeR, fda.usc, fgsea, ggalluvial, ggpubr, ggrepel, ggridges,
        ggseqlogo, graphkernels, graphlayouts, grid, gridExtra,
        harmony, igraph, iNEXT, IRanges, limma, keras, kmer, knitr,
        magrittr, Matrix.utils, methods, monocle3, msigdbr, naivebayes,
        org.Hs.eg.db, org.Mm.eg.db, Peptides, phangorn, pheatmap,
        phytools, pROC, ProjecTILs, protr, purrr, r3dmol, randomForest,
        RColorBrewer, readbitmap, readr, readxl, reticulate,
        rstudioapi, rlang, Rtsne, scales, scuttle, SeuratWrappers,
        SingleCellExperiment, slingshot, ssh, SummarizedExperiment,
        stringdist, tensorflow, tidygraph, tidytree, tidyselect, umap,
        vanddraabe, vegan, viridis, xgboost, yardstick, testthat (>=
        3.0.0)
Additional_repositories: https://vickreiner.github.io/drat/
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.1.1
VignetteBuilder: knitr
LazyData: true
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2022-08-14 16:19:41 UTC; vickr
Author: Alexander Yermanos [aut, cre],
  Andreas Agrafiotis [ctb],
  Raphael Kuhn [ctb],
  Danielle Shlesinger [ctb],
  Jiami Han [ctb],
  Tudor-Stefan Cotet [ctb],
  Victor Kreiner [ctb]
Repository: CRAN
Date/Publication: 2022-08-15 07:20:20 UTC
Built: R 4.2.0; ; 2022-08-16 13:38:54 UTC; unix
