Python packages
- tinytopics
GPU-accelerated topic modeling via sum-to-one constrained neural Poisson NMF
PyPI | GitHub - tinyvdiff
Minimalist visual regression testing plugin for pytest
PyPI | GitHub - py-ggsci
Scientific journal and sci-fi themed color palettes for plotnine
PyPI | GitHub - pytest-r-snapshot
A pytest plugin for snapshot testing against R reference outputs
PyPI | GitHub - py-pkglite
A simple framework for packing source packages written in any programming language into a text file and restoring them into the original directory structure
PyPI | GitHub - rtflite
Lightweight RTF composer for Python
PyPI | GitHub - gsdesign-python
Group sequential design for Python (experimental)
PyPI | GitHub - simtrial-python
Clinical trial simulation for Python (experimental)
PyPI | GitHub
R packages
Infrastructure and automation
- pkglite
Compact package representations
CRAN | GitHub | Paper - pkgdown.offline
Build pkgdown websites without an internet connection
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
CRAN | 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 - ssw-r
R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
CRAN | GitHub - grex
Gene ID mapping for Genotype-Tissue Expression (GTEx) data
CRAN | GitHub - tidychem
Read, preprocess, and featurize chemical data using RDKit
GitHub - cats
Joint power analysis for non-symmetric two-stage case-control designs
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
Rust packages
- revdeprun
Easy reverse dependency checks for R with cloud-ready environment setup
crates.io | docs.rs | GitHub - gsdesign-rust
Group sequential design for Rust (experimental)
crates.io | GitHub - simtrial-rust
Clinical trial simulation for Rust (experimental)
crates.io | GitHub
VS Code extensions
- vscode-textmate-rstheme
A light theme for Visual Studio Code inspired by the TextMate (default) theme in RStudio IDE
GitHub repository - vscode-markdown-stupefy
Convert smart punctuation to ASCII
GitHub repository
JavaScript apps
- Deep Learning GPU Selector
Discover the best GPU for your deep learning needs by answering a few yes/no questions
GitHub | Blog post - Word Cloud Generator (Batteries Included)
A fork version of Jason Davies’ word cloud generator with color palette selection and updated default values
GitHub | Blog post - font-overlay
Interactively compare typesetting characteristics between fonts across customizable text, font size, letter spacing, and optical size.
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 - 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
Browser extensions
- Unsplash Landscape
A Chrome extension that hides Unsplash+ photos and shows only landscape images from Unsplash.
Machine learning workflows
- exp2vec
Workflow for training tissue-specific gene embeddings on GTEx data - bcpm-msaenet
Workflow 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
Workflow 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 - ChromaClust
Image color topic modeling using fastTopics.
The original idea was from my final project (poster) for the course HGEN 48600/STAT 35450.
Open source contributions
- gsDesign
Group sequential clinical trial design, largely as presented in Jennison and Turnbull (2000)
CRAN | GitHub | gsDesign: 15 Years of Development in 5 Minutes (4K 60fps) - gsDesign Shiny app
Web application for group sequential clinical trial design
Mirror 1 | Mirror 2 - gsDesign2
Group sequential design with non-constant effect
CRAN | GitHub - simtrial
Clinical trial simulation
CRAN | GitHub - gMCPLite
Lightweight fork of gMCP for graph-based multiple comparison procedures
CRAN | GitHub - gMCPShiny
Shiny app for graphical multiplicity control
GitHub - r2rtf
Create production-ready Rich Text Format (RTF) tables and figures
CRAN | GitHub - metalite
Unified data structure for metadata information in clinical analysis & reporting (A&R), leveraging the Analysis Data Model (ADaM) datasets for consistent and accurate metadata representation
CRAN | GitHub - metalite.ae
Analyzes adverse events in clinical trials using the metalite data structure. Simplifies the workflow to create production-ready tables, listings, and figures discussed in the adverse events analysis chapters of R for Clinical Study Reports and Submission.
CRAN | GitHub - boxly
Interactive box plot using plotly for clinical data analysis
CRAN | GitHub - forestly
Interactive forest plot for clinical trial safety analysis using metalite, reactable, plotly, and Analysis Data Model (ADaM) datasets
CRAN | GitHub - 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
Awesome lists and code recipes
- awesome-shiny-extensions
A curated list of R packages that offer extended UI or server components for Shiny - awesome-webr
A curated list of awesome resources for learning WebR, a version of the statistical language R compiled for the browser and Node.js using WebAssembly - r-base-shortcuts
A collection of lesser-known base R idioms and shortcuts for writing concise and fast base R code - r-rust-pkgs
R packages using Rust on CRAN - r-future-recipes
Guides and examples for the R future framework for parallel computing - r-windows-paths
Key R toolchain paths for Windows systems - deep-learning-recipes
R implementation for selected machine learning methods with deep learning frameworks - llm-cliches
A collection of commonly used clichés and phrases in Large Language Models (LLMs) outputs.
Hugo/blogdown themes
- hugo-tanka
A minimalist theme for Hugo and blogdown
Live Preview | 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 - hugo-nanx2023
A minimalist Bootstrap 5 theme for Hugo and blogdown - hugo-nanx2026
A minimalist Tailwind CSS theme for Hugo and blogdown
Fonts
- DM Mono Ligaturized
DM Mono font with Fira Code ligatures - Noto Sans Mono Ligaturized
Noto Sans Mono font with Fira Code ligatures - Instrument Sans Modded
Instrument Sans font with modified glyphs (uppercase R leg placement, flat head lowercase t)
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)