README.md

In wangshisheng/motifeR2.0: motifeR 2.0: improving analysis and annotation of protein post-translational modification motifs

motifeR 2.0

motifeR 2.0: improving analysis and annotation of protein post-translational modification motifs

Brief Description

motifeR 2.0 is a web-based tool, which possesses the core functions as previously implemented in the first version motifeR published in 2019 with an addition of several new features, including:1. Mapping the PTM site and protein sequences and identifiers between non-human species and H. sapiens; 2. Calculating sequence window similarity and allowing thresholds of similarity filtering for motif mapping; 3. Offering more flexible annotation based on kinase-substrate databases (e.g. PhosphoSitePlus) and network plots; 4. Visualizing the expression of modification sites on interacting proteins on the basis of public or user-uploaded protein-protein interaction data. This software is available here: https://yslproteomics.shinyapps.io/motifeR2.

Graphical Abstract

How to use

A detailed introduction of this software can be found in the Help part of this tool: https://yslproteomics.shinyapps.io/motifeR2. And if you want to install this software locally, please check below.

Run it locally

This tool is developed with R, so if you want to run it locally, you may do some preparatory work: 1. Install R. You can download R from here: https://www.r-project.org/. 2. Install RStudio. (Recommendatory but not necessary). You can download RStudio from here: https://www.rstudio.com/. 3. Check packages. After installing R and RStudio, you should check whether you have installed these packages (devtools,shiny,shinyBS,shinyjs,shinyWidgets,DT,gdata,knitr,ggplot2,ggsci,openxlsx,data.table,Biostrings,stringi,stringr,ggrepel,igraph,ggraph,graphlayouts,scales,scatterpie,plotfunctions,mapplots,impute,tidyr,msa). You may run the codes below to check them:

if(!require(pacman)) install.packages("pacman")
pacman::p_load(devtools,shiny,shinyBS,shinyjs,shinyWidgets,DT,gdata,knitr,ggplot2,ggsci,openxlsx,data.table,Biostrings,stringi,stringr,ggrepel,igraph,ggraph,graphlayouts,scales,scatterpie,plotfunctions,mapplots,impute,tidyr,msa)

4. Install packages locally. motifeR needs two more packages (rmotifx and ggseqlogo), however, the functions in the two packages are not enough. I update some functions, and you should download and then install them locally.

rmotifx: download from here: https://github.com/wangshisheng/motifeR/blob/master/rmotifx_1.0.tar.gz. ggseqlogo: download from here: https://github.com/wangshisheng/motifeR/blob/master/ggseqlogo_0.1.tar.gz.

After downloading them, set the path where the packages are:

setwd('path') #path is where the two packages are.
install.packages("rmotifx_1.0.tar.gz", repos = NULL,type="source")
install.packages("ggseqlogo_0.1.tar.gz", repos = NULL,type="source")

If the preparatory work has been done, you can run this tool locally as below:

if(!require(motifeR2)) devtools::install_github("wangshisheng/motifeR2.0")
library(motifeR2)
motifeR2_app()

Then motifeR will be started as below:

Friendly suggestion

1. Open motifeR 2.0 with Chrome, Mozilla Firefox, Safari or Firefox.
2. The minimum operating system specifications are: RAM 4GB, Hard drive 100 GB.

Contact

You could push an issue on this github. And optionally, please feel free to sent me an e-mail if you have any question or find a bug about this tool. Thank you^_^ Email: [e-mail].

wangshisheng/motifeR2.0 documentation built on Dec. 23, 2021, 5:07 p.m.