README.md

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

Yeskit (Yet another single-cell analysis toolkit)

Yeskit is an R package designed for single-cell gene expression data importation, integration, clustering, differential analysis, functional analysis, and visualization. Since Yeskit does not change the default data structure of Seurat, it can be easily integrated into most existing scRNA-seq analysis workflows.

Yeskit can be used to read other information (such as gene mutation-by-cell matrix, pathogen count-by-cell matrix) and store them as additional data in the Seurat obj@metadata slot. In addition, Yeskit also has the function of reading and distinguishing the source of cells from the scRNA-seq data of xenografts samples (PDX model).

When there are many points in the vector diagram, editing becomes difficult. To this end, most visualization functions in Yeskit have the option to rasterize the geom_point layer of ggplot2 and keep all axes, labels, and text in vector format. The detailes are described in our paper PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19.

Installation

Yeskit package can be easily installed under the following instruction:

devtools::install_github("ncrna/Yeskit")

Vignettes

Please check the following link to get a rapid understanding about Yeskit:

Walkthrough - Decoding Intracellular Pathogens of H3N2 at the Single-Cell level using Yeskit

Troubleshooting

In a particular case, the Cairo package can be loaded but crashes the R process when called. This is probably the case that the version of Cairo was built with an older version of R. Try the following instruction:

BioManager::install("Cairo", force = TRUE)

For OS X users, you may happen to an error like this:

Error : .onLoad failed in loadNamespace() for ‘Cairo’
... 
Library not loaded: /opt/X11/lib/libXrender.1.dylib

The reason is X11 doesn't ship with OS X any more, users can download and install XQuartz from https://www.xquartz.org to solve this problem.

Help

If you have any questions/problems with Yeskit, feel free to leave an issue! We will try our best to provide support, address new issues, and keep improving this package.

Citation

Wei Zhang, Xiaoguang Xu, Ziyu Fu, Jian Chen, Saijuan Chen, Yun Tan. PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19. Front. Med., https://doi.org/10.1007/s11684-021-0915-9

The preprint version can be found here.

ncrna/Yeskit documentation built on Nov. 4, 2024, 10:32 p.m.