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: 3.2.3
Depends: R (≥ 3.5.0)
Imports: BiocGenerics, Biostrings, dplyr, ggplot2, knitr, jsonlite, Matrix, plyr, reshape2, rmarkdown, seqinr, Seurat, SeuratObject, stringr, tibble, tidyr, utils, useful
Suggests: AnnotationDbi, ape, circlize, cowplot, data.table, doParallel, fda.usc, fgsea, ggrepel, ggridges, ggseqlogo, grid, gridExtra, harmony, igraph, IRanges, limma, keras, methods, msigdbr, org.Mm.eg.db, pheatmap, phytools, purrr, scales, SummarizedExperiment, stringdist, tensorflow, vegan, testthat (≥ 3.0.0)
Published: 2021-10-19
Author: Alexander Yermanos [aut, cre], Andreas Agrafiotis [ctb], Raphael Kuhn [ctb], Victor Kreiner [ctb], Damiano Robbiani [ctb], Josephine Yates [ctb], Jiami Han [ctb], Chrysa Papadopoulou [ctb], C├ędric Weber [ctb], Danielle Shlesinger [ctb], Raphael Dizerens [ctb]
Maintainer: Alexander Yermanos <ayermanos at gmail.com>
License: GPL-2
NeedsCompilation: no
Materials: README
CRAN checks: Platypus results

Documentation:

Reference manual: Platypus.pdf
Vignettes: PlatypusV3 AgedCNS vignette

Downloads:

Package source: Platypus_3.2.3.tar.gz
Windows binaries: r-devel: Platypus_3.2.3.zip, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): Platypus_3.2.3.tgz, r-release (x86_64): Platypus_3.2.3.tgz, r-oldrel: Platypus_3.2.3.tgz

Linking:

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