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. 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年10月18日
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>
NeedsCompilation:
no
Documentation:
Downloads:
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