A collection of my R packages for machine learning, data visualization, and reproducible research.
msaenet: Multi-Step Adaptive Estimation Methods for Reducing False Positive Selection in Sparse Regressions
Implements the multi-step adaptive elastic-net (MSAENet) algorithm for feature selection in
high-dimensional regressions. Also supports multi-step adaptive estimation based on MCP-net/SCAD-net.
ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2
Offers a collection of ggplot2 color palettes inspired by scientific journals,
data visualization libraries, science fiction movies, and TV shows.
liftr: Containerize R Markdown Documents
liftr aims to solve the problem of persistent reproducible reporting.
To achieve this goal, it extends the R Markdown metadata format,
and uses Docker to containerize and render R Markdown documents.
protr: R Package for Generating Various Numerical Representation Schemes of Protein Sequence
R package generating various numerical representation schemes of protein sequence for bioinformatics
and proteochemometrics research.
Rcpi: R/Bioconductor Package for Generating Various Descriptors of Proteins, Compounds, and their Interactions
The Rcpi package emphasizes the comprehensive integration of
bioinformatics and chemoinformatics into a molecular informatics platform for drug discovery.
OHPL: Ordered Homogeneity Pursuit Lasso for Group Variable Selection
Ordered homogeneity pursuit lasso (OHPL) algorithm for group variable selection.
The OHPL method takes the homogeneity structure in high-dimensional data into account
and enjoys the grouping effect to select groups of important variables automatically.
This feature makes it particularly useful for high-dimensional datasets with strongly
correlated variables, such as spectroscopic data.
hdnom: Benchmarking and Visualization Toolkit for Penalized Cox Models
hdnom creates nomogram visualizations for penalized Cox regression models,
with the support of reproducible survival model building, validation, calibration,
and comparison for high-dimensional data.
sevenbridges-r: Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
R client and utilities for Seven Bridges platform API, from Cancer
Genomics Cloud to other Seven Bridges supported platforms.
enpls: R Package for Ensemble Partial Least Squares Regression
Algorithmic framework for measuring feature importance, outlier detection,
model applicability evaluation, and ensemble predictive modeling with (sparse)
partial least squares regressions.
RECA: R Package for Relevant Component Analysis (RCA) in Supervised Distance Metric Learning
Relevant Component Analysis (RCA) tries to find a linear transformation of the feature space
such that the effect of irrelevant variability is reduced in the transformed space.
grex: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
grex offers a minimal dependency solution for mapping Ensembl gene IDs to
Entrez IDs, HGNC gene symbols, and UniProt IDs, for Genotype-Tissue Expression (GTEx) data.
A collection of my Shiny apps for interactive data analysis.
DockFlow: Bioconductor Workflow Containerization and Orchestration with liftr
Proof-of-concept project exploring the technical possibility and complexity
for bioinformatics workflow containerization and orchestration using Docker
All 18 available Bioconductor workflows were containerized.
hdnom.io: Web Application for Building Nomograms with High-Dimensional Data
hdnom.io is the web application for the hdnom package.
All the 9 model types in the hdnom package are supported.
It streamlined the process of nomogram building, model validation,
model calibration, and reproducible report generation.
This app has been selected as one of the
Shiny User Showcase.
TargetNet: Shiny Web Application for Drug Target Identification with Large-Scale Public Binding Affinities Data
Web application for predicting the binding probability of 623 potential drug
targets for given molecule(s).
Driven by machine learning modeling of large-scale public chemogenomics data.
ProtrWeb: Shiny Web Application for Computing Protein Sequence-Derived Descriptors
Web application for computing 14 types of protein sequence-derived structural and
physicochemical features in bioinformatics.
ImgSVD: Shiny Web Application for Image Compression via Singular Value Decomposition
ImgSVD is a Shiny app for image compression via singular value decomposition (SVD).
ImgSVD is inspired by Yihui Xie's comment in
Yixuan Qiu's article
on image compression via singular value decomposition with the R package
Signify: Shiny Web Application for Making Your p-value Sound Significant
Signify is a Shiny-based web application for making your (>0.05) p-values
The application is powered by the data from
I contributed some code to the following open source software.
- ashr - Methods for adaptive shrinkage, using Empirical Bayes.
- dml - A collection of distance metric learning algorithms in R.
- mxnet-r - A flexible and efficient machine learning library for heterogeneous distributed systems.
Themes for Hugo and Blogdown.
Renga: A Clean Bootstrap 4 Theme for Hugo and Blogdown
Offers a balance between minimalism and flexibility. Publish new content
quickly with simple Markdown, or construct complex pages by writing
HTML with Bootstrap 4.
Tanka: A Minimalist Theme for Hugo and Blogdown
A minimalist, text-oriented, and performant blog theme for Hugo/blogdown.
R Document Archives
An archive of some old R related documents.
使用 R 和 Apache 开发 Web 应用程序
Developing Web Applications with R and Apache
来自 Google 的 R 语言编码风格指南
Google's R Style Guide