README.md

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

==> Platypus and PlatypusDB homepage

Platypus

Platypus is an R toolkit designed to facilitate the data analysis of single-cell immune repertoire sequencing experiments. The manuscript corresponding to Platypus v2 can be found here at Yermanos et al NARGAB 2021 https://doi.org/10.1093/nargab/lqab023 and the updated manuscript concerning the v3 Platypus ecosystem can be found here: https://www.biorxiv.org/content/10.1101/2022.09.28.509709v1

Ongoing updates in the Platypus pipeline (v3)

Due to the recent changes of the default clonotyping strategy in Cellranger (version 5 and version 6) and annotation of the framework and CDR regions (version 7) we have rebuild Platypus to revolve around the VDJ_build function. This function creates a dataframe of the repertoire data. The function VGM_build integrates the repertoire and transcriptome information (Seurat object) and will serve as the input to all secondary functions in future iterations of the package. The advantage of this is having all repertoire and transcriptome information at a per-cell level.

Furthermore we developed PlatypusDB, a publicly available database that facilitates the download, integration, and analysis of hundred thousands of single-cells that contain GEX information, VDJ information or both. With a single line of code, PlatypusDB allows users to either download and explore available datasets or integrate existing experiments with their own datasets. Collectively, PlatypusDB serves as a database for the scientific community interested in exploration of single cell immune repertoire sequencing experiments from mouse and human.

Stay tuned for updates https://twitter.com/alexyermanos?lang=en

Architecture

System requirements

Platypus has been successfully installed on MacOS X (v10.14.6) and Windows 10 Pro (v1909), and used on R versions 4.4.0, 4.0.0 and 3.6.1

Installation

Platypus can easily be installed from CRAN or Github. As changes and bugfixes are made regularly, the Github version may be more recent.

Please scroll down for instructions on how to install the necessary dependencies.

### Removing any previous versions of the package
# First we will ensure that there is no previous version installed locally
#detach("package:Platypus", unload=TRUE)
#remove.packages("Platypus")

### Downloading and installing Platypus from CRAN

install.packages("Platypus")

### Downloading and installing Platypus from Github

# First we need to download the most recent version from the master branch at https://github.com/alexyermanos/Platypus we can install the package using the following command.
# WARNING: This needs to be replaced with your own directory where the downloaded package is found
# For MacOS users it may look like this
install.packages("~/Downloads/Platypus_3.6.0.tar.gz", repos = NULL, type="source")
# For windows it will likely look something like this.
# WARNING: You will need to replace 'YourPCName' with your user name for the windows account in the directory.
install.packages("C:/Users/YourPCName/Downloads/Platypus_3.6.0.tar.gz", repos = NULL, type="source")

# The individual R functions can additionally be found on the github in the Functions branch. Within this branch, there is a folder "R" which contains the individual functions. This can similarly be downloaded and loaded into the R environment incase not all functions are desired. Similarly, these functions are actively updated and may include more features than the in current CRAN version.

Platypus uses a number of different R packages, some of which need prior installation. These can be installed either from CRAN, Bioconductor:

CRAN

Code to install the packages from CRAN:

#Essential packages
install.packages("tidyverse")
install.packages("Seurat")
install.packages("utils")

#Optional packages needed for some individual functions
install.packages("ape")
install.packages("circlize")
install.packages("do")
install.packages("dplyr")
install.packages("ggplot2")
install.packages("ggseqlogo")
install.packages("igraph")
install.packages("jsonlite")
install.packages("phytools")
install.packages("reshape2")
install.packages("seqinr")
install.packages("stringdist")

GitHub

Harmony (but not required if not using the Harmony integration method)

Code for installing harmony:

install.packages("devtools")
library(devtools)
install_github("immunogenomics/harmony")

##Bioconductor Code for installing the packages from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")
BiocManager::install("org.Mm.eg.db")
BiocManager::install("edgeR")
BiocManager::install("fgsea")
BiocManager::install("msa")
BiocManager::install("ggtree")

Please post any questions or issues in the respecitve github section: https://github.com/alexyermanos/Platypus/issues Please reach out to us with any questions or if you would like to contribute.

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.