R packages

I build R packages to improve my workflow.

Infrastructure and automation

• pkglite
  Compact package representations
  CRAN | GitHub

Statistical machine learning

• msaenet
  Multi-step adaptive estimation for sparse regressions
  CRAN | GitHub | Paper
• stackgbm
  Minimalist implementation of model stacking for gradient boosted tree models built by xgboost, lightgbm, and catboost
  GitHub
• oneclust
  Maximum homogeneity clustering for univariate data
  CRAN | GitHub
• logreg
  Regularized logistic regressions with computational graphs
  GitHub
• OHPL
  Ordered homogeneity pursuit lasso for group variable selection
  CRAN | GitHub | Paper
• RECA
  Relevant component analysis for supervised distance metric learning
  CRAN | GitHub
• enpls
  Ensemble partial least squares regression
  CRAN | GitHub

Statistical graphics and computing

• ggsci
  Scientific journal and sci-fi themed color palettes for ggplot2
  CRAN | GitHub
• liftr
  Containerize R Markdown documents
  CRAN | GitHub | Paper
• hdnom
  Benchmarking and visualization toolkit for penalized Cox models
  CRAN | GitHub | Paper

Bioinformatics and cheminformatics

• protr
  Protein sequence feature extraction
  CRAN | GitHub | Paper
• Rcpi
  Feature extraction for proteins, compounds, and their interactions
  Bioconductor | GitHub | Paper
• tidychem
  Read, preprocess, and featurize chemical data using RDKit
  GitHub
• grex
  Gene ID mapping for Genotype-Tissue Expression (GTEx) data
  CRAN | GitHub
• cats
  Joint power analysis for non-symmetric two-stage case-control designs
  GitHub
• ssw-r
  R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
  GitHub
• tidycwl
  Tidy Common Workflow Language tools and workflows
  CRAN | GitHub | Paper
• biocompute
  Create and manipulate BioCompute Objects
  CRAN | GitHub | Paper
• sevenbridges-r
  Seven Bridges API client
  Bioconductor | GitHub
• sbpack-r
  Pack and upload CWL apps to Seven Bridges powered platforms
  GitHub

Shiny apps

Shiny apps, widgets, and templates for interactive data analysis.

• shiny-loading-skeleton
  Shiny app template with an animated, fully customizable skeleton loader.
  Demo
• shiny-fcp-loader
  Shiny app template with a loading screen that aims to minimize the time to first contentful paint (FCP).
  Demo
• shiny-highlight-rmarkdown
  Syntax highlighting for R Markdown output in Shiny based on highlight.js
  Demo
• exp2vec-shiny
  Shiny app for gene neighbors and gene analogies discovery with tissue-specific gene embeddings training on GTEx data.
  Demo
• bco-app
  Create, validate, and browse BioCompute Objects. Advanced track winner of the precisionFDA challenge on BioCompute Objects.
  Documentation | Paper
• protrweb
  Compute protein sequence-derived descriptors
  Mirror 1 | Mirror 2 | Paper
• targetnet
  Drug target identification with large-scale binding affinities data
  Mirror 1 | Mirror 2
• imgsvd
  Image compression via singular value decomposition
  Mirror 1 | Mirror 2
• hdnom-app
  Benchmarking and visualization of penalized Cox models
  Mirror 1 | Mirror 2
• conjugate-normal-umkv
  A demo of Bayesian inference for normal mean (known variance)
  Mirror 1 | Mirror 2
• signify
  Make your (>0.05) p-values “sound significant”
  Mirror 1 | Mirror 2
• cwl-formatter
  Format Common Workflow Language (CWL) apps
  Mirror 1
• cwl-exploder
  Unpack monolithic CWL workflows
  Mirror 1
• cwl-upgrader
  Upgrade CWL apps from sbg:draft2 to v1.0
  Mirror 1

Data analysis pipelines

Reusable pipelines for analyzing real-world datasets in specific domains.

• exp2vec
  Pipeline for training tissue-specific gene embeddings on GTEx data.
• bcpm-msaenet
  Pipeline for the precisionFDA challenge on brain cancer predictive modeling and biomarker discovery. The 2nd place solution by predictive performance. Features multi-step adaptive SCAD-net and relaxed stability selection for feature selection, and a two-layer stacking tree model with xgboost, lightgbm, and catboost.
• rankv
  Pipeline for the precisionFDA challenge on detecting adverse event anomalies using FDA open data. Features a rank aggregated signal detection method for Vaccine Adverse Event Reporting System (VAERS) data, with base signal detection methods including Gamma Poisson Shrinker, PRR, ROR, and BCPNN.
  Website

Code contributor

• gMCPLite
  Lightweight fork of gMCP for graph-based multiple comparison procedures
  CRAN
• gsDesign Shiny app
  Group sequential clinical trial design
  Mirror 1 | Mirror 2
• PDXNet Portal
  Patient-derived xenograft (PDX) model, data, workflow, and tool discovery
  Paper
• ashr
  Methods for adaptive shrinkage, using Empirical Bayes
  CRAN | Paper
• dml
  Distance metric learning in R
  CRAN | Paper

Code recipes & awesome lists

• awesome-shiny-extensions
  A curated list of R packages that offer extended UI or server components for Shiny.
• deep-learning-recipes
  R implementation for selected machine learning methods with deep learning frameworks.

Hugo/blogdown themes

• hugo-tanka
  A minimalist theme for Hugo and blogdown
  Live Preview | Hugo Themes | blogdown book
• hugo-renga
  A clean Bootstrap 4 theme for Hugo and blogdown
  Live Preview
• hugo-nanx2020
  An opinionated Bootstrap 4 theme for Hugo and blogdown
• hugo-nanx2021
  A minimalist Bootstrap 5 theme for Hugo and blogdown
• hugo-nanx2022
  A minimalist Bootstrap 5 theme for Hugo and blogdown

Collections

• dockflow.org
  Bioconductor workflow containerization with liftr
  GitHub
• nanx.app
  A collection of shiny apps built by me
  GitHub

Archives

• 使用 R 和 Apache 开发 Web 应用程序 (2011)
• 来自 Google 的 R 语言编码风格指南 (2011)