Shixiang Wang

软件包与工具

这个页面列出了我(参与)开发的软件包和工具。

R 包

ezcox

CRANstatus HitCount AppVeyor buildstatus Travis buildstatus Codecov testcoverage Lifecycle:maturing

主页: 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

lifecycle GitHubtag

主页: 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

CRANstatus Lifecycle:experimental AppVeyor buildstatus Travis buildstatus Coveragestatus

主页: 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

CRANstatus lifecycle AppVeyor buildstatus Travis buildstatus Coveragestatus

主页: https://github.com/ShixiangWang/sigminer

The goal of sigminer is to provide a uniform interface for genomic variation signature analysis and visualization.

UCSCXenaTools

CRAN AppVeyor BuildStatus Travis buildstatus

CoverageStatus GitHubissues Closedissues

主页: 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.

文档:

UCSCXenaShiny

CRANstatus lifecycle Travis buildstatus AppVeyor buildstatus Coveragestatus

主页: 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

AppVeyor build status Travis build status Lifecycle: maturing CRAN status

主页: 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).

文档:

copynumber

HitCount

主页: https://github.com/ShixiangWang/copynumber

This package is a fork of Bioconductor R package ‘copynumber’ with minor modification for supporting hg38 genome assembly.

Python 包

loon

GitHub repo size PyPI pylint Documentation Status Downloads HitCount GitHub issues GitHub last commit

主页: 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 工具

sync-deploy

DOI Open Source Love svg1 MIT license Maintenance

主页: 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

主页: 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

主页: 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 插件

flymaps

主页: 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.