Software and Tool
This page lists all softwares and tools I developed.
R packages
ezcox
Homepage: https://github.com/ShixiangWang/ezcox
The goal of ezcox is to operate a batch of univariate or multivariate Cox models and return tidy result.
DoAbsolute
Homepage: https://github.com/ShixiangWang/DoAbsolute
The goal of DoAbsolute is to automate ABSOLUTE calling for multiple samples in parallel way.
ABSOLUTE is a famous software developed by Broad Institute, however, the RunAbsolute function is designed for computing one sample each time and set no default values. DoAbsolute helps user set default parameters according to ABSOLUTE documentation, provides a uniform interface to input data easily and runs RunAbsolute parallelly.
metawho
Homepage: https://github.com/ShixiangWang/metawho
The goal of metawho is to provide simple R implementation of “Meta-analytical method to Identify Who Benefits Most from Treatments”.
metawho is powered by R package metafor and does not support dataset contains individuals for now. Please use Stata package ipdmetan if you are more familiar with Stata code.
sigminer
Homepage: https://github.com/ShixiangWang/sigminer
The goal of sigminer is to provide a uniform interface for genomic variation signature analysis and visualization.
UCSCXenaTools
Homepage: https://github.com/ShixiangWang/UCSCXenaTools
UCSCXenaTools is an R package for downloading and exploring data from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Documentation:
UCSCXenaShiny
Homepage: https://github.com/openbiox/XenaShiny
UCSCXenaShiny is Shiny app for UCSC Xena, this package is built on the top of Shiny and UCSCXenaTools etc..
contribution
Homepage: https://github.com/ShixiangWang/contribution
The goal of contribution is to generate contribution table for credit assignment in a project. This is inspired by Nick Steinmetz (see twitter https://twitter.com/SteinmetzNeuro/status/1147241138291527681).
Documentation:
copynumber
Homepage: https://github.com/ShixiangWang/copynumber
This package is a fork of Bioconductor R package ‘copynumber’ with minor modification for supporting hg38 genome assembly.
Python packages
loon
Homepage: https://github.com/ShixiangWang/loon
loon is a Python toolkit for operating remote host based on SSH. Idea for developing loon comes from sync-deploy, which is limited by its pure bash code.
Linux tools
sync-deploy
Homepage: https://github.com/ShixiangWang/sync-deploy
sync-deploy is a shell toolkit for deploying script/command task on a remote host, including up/download files, run script and more.
Variants2Neoanitgen
Homepage: https://github.com/ShixiangWang/Variants2Neoantigen
Variants2Neoanitgen is a neoantigen calling pipeline begins from variants record file (MAF).
Of note, VCF file as input is not supported
install_GISTIC
Homepage: https://github.com/ShixiangWang/install_GISTIC
I have written two Chinese blogs for telling readers how to install GISTIC 2.0 (a famous software for copy numbeer analysis) step by step. Recently I realize the installation steps can be implemented automatically, so I write this program.
VSCode extensions
flymaps
Homepage: https://github.com/ShixiangWang/flymaps
Convenient keymaps for data science work with Python, R, Markdown and Rmarkdown in VS Code.
Currently, it is very simple.