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

DoAbsolute

lifecycle GitHub
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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

CRAN
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experimental AppVeyor build
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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

CRAN
status lifecycle AppVeyor build
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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 Build
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Coverage
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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

CRAN
status lifecycle Travis build
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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:

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