Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

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
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)
Published:	2022-08-15
Author:	Alexander Yermanos [aut, cre], Andreas Agrafiotis [ctb], Raphael Kuhn [ctb], Danielle Shlesinger [ctb], Jiami Han [ctb], Tudor-Stefan Cotet [ctb], Victor Kreiner [ctb]
Maintainer:	Alexander Yermanos <ayermanos at gmail.com>
License:	GPL-2
NeedsCompilation:	no
Additional_repositories:	https://vickreiner.github.io/drat/
Materials:	README NEWS
CRAN checks:	Platypus results

Documentation:

Reference manual:	Platypus.pdf
Vignettes:	PlatypusV3 AgedCNS vignette

Downloads:

Package source:	Platypus_3.4.1.tar.gz
Windows binaries:	r-devel: Platypus_3.4.1.zip, r-release: Platypus_3.4.1.zip, r-oldrel: Platypus_3.4.1.zip
macOS binaries:	r-release (arm64): Platypus_3.4.1.tgz, r-oldrel (arm64): Platypus_3.4.1.tgz, r-release (x86_64): Platypus_3.4.1.tgz, r-oldrel (x86_64): Platypus_3.4.1.tgz
Old sources:	Platypus archive

Linking:

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